Starting phenix.real_space_refine on Wed Jun 25 03:36:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h3n_0136/06_2025/6h3n_0136.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h3n_0136/06_2025/6h3n_0136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6h3n_0136/06_2025/6h3n_0136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h3n_0136/06_2025/6h3n_0136.map" model { file = "/net/cci-nas-00/data/ceres_data/6h3n_0136/06_2025/6h3n_0136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h3n_0136/06_2025/6h3n_0136.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 9339 2.51 5 N 2730 2.21 5 O 2817 1.98 5 H 14388 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29319 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9773 Classifications: {'peptide': 627} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 591} Chain breaks: 1 Chain: "B" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9773 Classifications: {'peptide': 627} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 31, 'TRANS': 591} Chain breaks: 1 Chain: "C" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9773 Classifications: {'peptide': 627} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 591} Chain breaks: 1 Time building chain proxies: 12.85, per 1000 atoms: 0.44 Number of scatterers: 29319 At special positions: 0 Unit cell: (91.3, 93.5, 182.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 O 2817 8.00 N 2730 7.00 C 9339 6.00 H 14388 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.66 Conformation dependent library (CDL) restraints added in 2.5 seconds 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 14.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 151 through 163 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 264 through 281 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 151 through 163 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 264 through 281 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 151 through 163 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 264 through 281 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 625 through 637 155 hydrogen bonds defined for protein. 348 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: 9.69 Time building geometry restraints manager: 9.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 14367 1.13 - 1.30: 2550 1.30 - 1.47: 6356 1.47 - 1.64: 6331 1.64 - 1.81: 69 Bond restraints: 29673 Sorted by residual: bond pdb=" CD2 PHE B 152 " pdb=" HD2 PHE B 152 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" CZ2 TRP C 98 " pdb=" HZ2 TRP C 98 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" CD1 PHE A 127 " pdb=" HD1 PHE A 127 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" CZ3 TRP A 141 " pdb=" HZ3 TRP A 141 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" CD1 PHE C 392 " pdb=" HD1 PHE C 392 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.51e+01 ... (remaining 29668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 48791 3.31 - 6.62: 4094 6.62 - 9.92: 400 9.92 - 13.23: 24 13.23 - 16.54: 4 Bond angle restraints: 53313 Sorted by residual: angle pdb=" C PRO A 638 " pdb=" N PRO A 639 " pdb=" CA PRO A 639 " ideal model delta sigma weight residual 119.66 127.34 -7.68 7.20e-01 1.93e+00 1.14e+02 angle pdb=" C PHE A 637 " pdb=" N PRO A 638 " pdb=" CA PRO A 638 " ideal model delta sigma weight residual 119.66 126.66 -7.00 7.20e-01 1.93e+00 9.46e+01 angle pdb=" C PHE B 637 " pdb=" N PRO B 638 " pdb=" CA PRO B 638 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.00e+01 angle pdb=" C GLY B 374 " pdb=" N PRO B 375 " pdb=" CA PRO B 375 " ideal model delta sigma weight residual 119.78 128.65 -8.87 1.03e+00 9.43e-01 7.41e+01 angle pdb=" C GLY C 374 " pdb=" N PRO C 375 " pdb=" CA PRO C 375 " ideal model delta sigma weight residual 119.78 128.62 -8.84 1.03e+00 9.43e-01 7.36e+01 ... (remaining 53308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 13210 16.78 - 33.57: 478 33.57 - 50.35: 194 50.35 - 67.14: 108 67.14 - 83.92: 26 Dihedral angle restraints: 14016 sinusoidal: 7665 harmonic: 6351 Sorted by residual: dihedral pdb=" CD2 HIS B 175 " pdb=" CG HIS B 175 " pdb=" ND1 HIS B 175 " pdb=" HD1 HIS B 175 " ideal model delta harmonic sigma weight residual 180.00 -147.20 -32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CD2 HIS B 209 " pdb=" CG HIS B 209 " pdb=" ND1 HIS B 209 " pdb=" HD1 HIS B 209 " ideal model delta harmonic sigma weight residual 180.00 156.25 23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CD2 HIS B 71 " pdb=" CG HIS B 71 " pdb=" ND1 HIS B 71 " pdb=" HD1 HIS B 71 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 14013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1099 0.054 - 0.107: 738 0.107 - 0.161: 244 0.161 - 0.215: 54 0.215 - 0.268: 7 Chirality restraints: 2142 Sorted by residual: chirality pdb=" CA TRP C 96 " pdb=" N TRP C 96 " pdb=" C TRP C 96 " pdb=" CB TRP C 96 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ARG C 502 " pdb=" N ARG C 502 " pdb=" C ARG C 502 " pdb=" CB ARG C 502 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA TRP A 96 " pdb=" N TRP A 96 " pdb=" C TRP A 96 " pdb=" CB TRP A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2139 not shown) Planarity restraints: 4569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 175 " -0.096 2.00e-02 2.50e+03 1.18e-01 3.12e+02 pdb=" CG HIS B 175 " -0.076 2.00e-02 2.50e+03 pdb=" ND1 HIS B 175 " -0.120 2.00e-02 2.50e+03 pdb=" CD2 HIS B 175 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 HIS B 175 " -0.057 2.00e-02 2.50e+03 pdb=" NE2 HIS B 175 " 0.035 2.00e-02 2.50e+03 pdb=" HD1 HIS B 175 " 0.274 2.00e-02 2.50e+03 pdb=" HD2 HIS B 175 " 0.095 2.00e-02 2.50e+03 pdb=" HE1 HIS B 175 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 209 " -0.088 2.00e-02 2.50e+03 9.05e-02 1.84e+02 pdb=" CG HIS B 209 " -0.050 2.00e-02 2.50e+03 pdb=" ND1 HIS B 209 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 HIS B 209 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 HIS B 209 " -0.048 2.00e-02 2.50e+03 pdb=" NE2 HIS B 209 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS B 209 " 0.210 2.00e-02 2.50e+03 pdb=" HD2 HIS B 209 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 HIS B 209 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 209 " -0.086 2.00e-02 2.50e+03 8.71e-02 1.71e+02 pdb=" CG HIS A 209 " -0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS A 209 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 HIS A 209 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 HIS A 209 " -0.045 2.00e-02 2.50e+03 pdb=" NE2 HIS A 209 " 0.022 2.00e-02 2.50e+03 pdb=" HD1 HIS A 209 " 0.202 2.00e-02 2.50e+03 pdb=" HD2 HIS A 209 " 0.071 2.00e-02 2.50e+03 pdb=" HE1 HIS A 209 " -0.066 2.00e-02 2.50e+03 ... (remaining 4566 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 3911 2.19 - 2.79: 57698 2.79 - 3.39: 81498 3.39 - 4.00: 117025 4.00 - 4.60: 172218 Nonbonded interactions: 432350 Sorted by model distance: nonbonded pdb=" O TRP C 98 " pdb=" HG1 THR C 101 " model vdw 1.587 2.450 nonbonded pdb=" O TRP B 98 " pdb=" HG1 THR B 101 " model vdw 1.591 2.450 nonbonded pdb=" O TRP A 98 " pdb=" HG1 THR A 101 " model vdw 1.593 2.450 nonbonded pdb=" OE1 GLU B 494 " pdb=" H GLU B 494 " model vdw 1.597 2.450 nonbonded pdb=" OE1 GLU C 402 " pdb=" H GLU C 402 " model vdw 1.598 2.450 ... (remaining 432345 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 9.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.530 Extract box with map and model: 1.110 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 62.960 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.015 0.067 15285 Z= 0.911 Angle : 1.517 16.538 20715 Z= 1.030 Chirality : 0.074 0.268 2142 Planarity : 0.010 0.162 2796 Dihedral : 10.777 83.921 5700 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.70 % Allowed : 4.65 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 1869 helix: 0.60 (0.36), residues: 192 sheet: 0.31 (0.21), residues: 528 loop : -0.72 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.006 TRP B 414 HIS 0.007 0.002 HIS B 186 PHE 0.019 0.004 PHE A 33 TYR 0.056 0.007 TYR A 138 ARG 0.009 0.001 ARG C 396 Details of bonding type rmsd hydrogen bonds : bond 0.13052 ( 155) hydrogen bonds : angle 4.59031 ( 348) covalent geometry : bond 0.01472 (15285) covalent geometry : angle 1.51686 (20715) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 2.431 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: 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: 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: 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 59 SER cc_start: 0.7932 (t) cc_final: 0.7208 (t) REVERT: A 132 ASP cc_start: 0.7244 (t0) cc_final: 0.6972 (p0) REVERT: A 246 ARG cc_start: 0.7439 (mmt180) cc_final: 0.7094 (mmp-170) REVERT: A 280 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7363 (tm-30) REVERT: A 356 LEU cc_start: 0.8802 (mt) cc_final: 0.8410 (mm) REVERT: B 33 PHE cc_start: 0.5004 (m-10) cc_final: 0.4736 (m-10) REVERT: B 80 VAL cc_start: 0.7290 (m) cc_final: 0.7046 (m) REVERT: B 378 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8045 (mm-30) REVERT: C 280 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7154 (tm-30) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.8616 time to fit residues: 510.8833 Evaluate side-chains 215 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 168 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 510 ASN B 454 GLN B 510 ASN C 510 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.153041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.119682 restraints weight = 45963.392| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.24 r_work: 0.3610 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15285 Z= 0.175 Angle : 0.585 5.670 20715 Z= 0.318 Chirality : 0.046 0.148 2142 Planarity : 0.006 0.049 2796 Dihedral : 4.722 19.161 2109 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.71 % Allowed : 8.24 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 1869 helix: 1.52 (0.37), residues: 189 sheet: -0.12 (0.21), residues: 513 loop : -0.22 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 96 HIS 0.006 0.001 HIS C 209 PHE 0.017 0.002 PHE A 154 TYR 0.013 0.002 TYR A 322 ARG 0.006 0.001 ARG B 302 Details of bonding type rmsd hydrogen bonds : bond 0.05173 ( 155) hydrogen bonds : angle 4.29178 ( 348) covalent geometry : bond 0.00392 (15285) covalent geometry : angle 0.58549 (20715) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 4.222 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: 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: symmetry clash REVERT: A 27 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6461 (mt-10) REVERT: A 132 ASP cc_start: 0.7473 (t0) cc_final: 0.7176 (p0) REVERT: A 246 ARG cc_start: 0.7968 (mmt180) cc_final: 0.7225 (mmm160) REVERT: A 280 GLN cc_start: 0.7827 (mm-40) cc_final: 0.6990 (tm-30) REVERT: A 356 LEU cc_start: 0.8544 (mt) cc_final: 0.8015 (mm) REVERT: A 636 MET cc_start: 0.8775 (mmp) cc_final: 0.8342 (tpp) REVERT: A 637 PHE cc_start: 0.7964 (m-80) cc_final: 0.7714 (m-10) REVERT: B 341 GLU cc_start: 0.8362 (tt0) cc_final: 0.8087 (tt0) REVERT: B 502 ARG cc_start: 0.7449 (mmm-85) cc_final: 0.7148 (ttt90) REVERT: C 56 MET cc_start: 0.7591 (ttm) cc_final: 0.7355 (ttm) REVERT: C 76 ARG cc_start: 0.8578 (ttp-110) cc_final: 0.8324 (ptm-80) REVERT: C 253 TYR cc_start: 0.7717 (m-80) cc_final: 0.7415 (m-80) REVERT: C 270 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6949 (mm-40) REVERT: C 280 GLN cc_start: 0.7844 (mm-40) cc_final: 0.6816 (tm-30) REVERT: C 469 MET cc_start: 0.7815 (ttt) cc_final: 0.7595 (ttp) REVERT: C 488 GLU cc_start: 0.7848 (tp30) cc_final: 0.7526 (tp30) outliers start: 27 outliers final: 22 residues processed: 254 average time/residue: 0.9211 time to fit residues: 336.4254 Evaluate side-chains 210 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 527 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 74 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN C 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.149690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.116479 restraints weight = 46853.280| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.25 r_work: 0.3573 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15285 Z= 0.169 Angle : 0.522 5.914 20715 Z= 0.276 Chirality : 0.045 0.146 2142 Planarity : 0.005 0.042 2796 Dihedral : 4.538 18.177 2109 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.52 % Allowed : 9.32 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 1869 helix: 1.89 (0.38), residues: 192 sheet: -0.42 (0.21), residues: 513 loop : -0.19 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 96 HIS 0.005 0.001 HIS C 209 PHE 0.015 0.001 PHE A 154 TYR 0.011 0.001 TYR C 143 ARG 0.011 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 155) hydrogen bonds : angle 4.15006 ( 348) covalent geometry : bond 0.00367 (15285) covalent geometry : angle 0.52190 (20715) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 2.189 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: 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: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7521 (t0) cc_final: 0.7231 (p0) REVERT: A 246 ARG cc_start: 0.7933 (mmt180) cc_final: 0.7231 (mmm160) REVERT: A 280 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7118 (tm-30) REVERT: A 356 LEU cc_start: 0.8652 (mt) cc_final: 0.8225 (mm) REVERT: A 636 MET cc_start: 0.8761 (mmp) cc_final: 0.8439 (tpp) REVERT: B 27 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6828 (mt-10) REVERT: B 253 TYR cc_start: 0.7596 (m-80) cc_final: 0.7315 (m-80) REVERT: C 76 ARG cc_start: 0.8728 (ttp-110) cc_final: 0.8494 (ptm-80) REVERT: C 253 TYR cc_start: 0.7825 (m-80) cc_final: 0.7509 (m-80) REVERT: C 280 GLN cc_start: 0.7767 (mm-40) cc_final: 0.6772 (tm-30) REVERT: C 469 MET cc_start: 0.7836 (ttt) cc_final: 0.7626 (ttp) REVERT: C 488 GLU cc_start: 0.7927 (tp30) cc_final: 0.7614 (tp30) outliers start: 24 outliers final: 20 residues processed: 212 average time/residue: 0.7121 time to fit residues: 219.0952 Evaluate side-chains 196 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 527 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 16 optimal weight: 1.9990 chunk 92 optimal weight: 0.0570 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.143746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.111215 restraints weight = 48073.777| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.24 r_work: 0.3494 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15285 Z= 0.135 Angle : 0.487 5.924 20715 Z= 0.253 Chirality : 0.044 0.146 2142 Planarity : 0.004 0.037 2796 Dihedral : 4.358 17.975 2109 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.33 % Allowed : 10.39 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1869 helix: 2.22 (0.38), residues: 192 sheet: -0.61 (0.21), residues: 513 loop : -0.11 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.005 0.001 HIS C 209 PHE 0.013 0.001 PHE A 154 TYR 0.010 0.001 TYR C 143 ARG 0.005 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 155) hydrogen bonds : angle 3.99585 ( 348) covalent geometry : bond 0.00298 (15285) covalent geometry : angle 0.48731 (20715) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 2.226 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: 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 132 ASP cc_start: 0.7560 (t0) cc_final: 0.7204 (p0) REVERT: A 246 ARG cc_start: 0.7933 (mmt180) cc_final: 0.7223 (mmm160) REVERT: A 280 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7158 (tm-30) REVERT: A 636 MET cc_start: 0.8779 (mmp) cc_final: 0.8487 (tpp) REVERT: B 27 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6910 (mt-10) REVERT: B 46 LEU cc_start: 0.8207 (tp) cc_final: 0.7837 (tt) REVERT: B 253 TYR cc_start: 0.7682 (m-80) cc_final: 0.7429 (m-80) REVERT: B 483 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8298 (m110) REVERT: C 253 TYR cc_start: 0.7888 (m-80) cc_final: 0.7608 (m-80) REVERT: C 280 GLN cc_start: 0.7784 (mm-40) cc_final: 0.6853 (tm-30) REVERT: C 469 MET cc_start: 0.7875 (ttt) cc_final: 0.7654 (ttp) REVERT: C 636 MET cc_start: 0.8664 (mmp) cc_final: 0.8378 (mmm) outliers start: 21 outliers final: 12 residues processed: 200 average time/residue: 0.6905 time to fit residues: 199.2382 Evaluate side-chains 180 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 107 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 158 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 264 GLN C 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.140124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.107736 restraints weight = 49073.738| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.29 r_work: 0.3464 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15285 Z= 0.157 Angle : 0.485 6.036 20715 Z= 0.252 Chirality : 0.044 0.145 2142 Planarity : 0.004 0.033 2796 Dihedral : 4.316 18.255 2109 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.58 % Allowed : 11.03 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 1869 helix: 2.23 (0.38), residues: 192 sheet: -0.85 (0.21), residues: 519 loop : -0.17 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 213 HIS 0.005 0.001 HIS C 209 PHE 0.017 0.001 PHE A 592 TYR 0.010 0.001 TYR B 143 ARG 0.007 0.000 ARG C 308 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 155) hydrogen bonds : angle 3.97532 ( 348) covalent geometry : bond 0.00346 (15285) covalent geometry : angle 0.48467 (20715) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 2.109 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7551 (t0) cc_final: 0.7269 (p0) REVERT: A 246 ARG cc_start: 0.8058 (mmt180) cc_final: 0.7350 (mmm160) REVERT: A 280 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7177 (tm-30) REVERT: A 519 ASP cc_start: 0.8227 (t0) cc_final: 0.7462 (m-30) REVERT: A 636 MET cc_start: 0.8807 (mmp) cc_final: 0.8527 (tpp) REVERT: B 27 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6929 (mt-10) REVERT: B 46 LEU cc_start: 0.8102 (tp) cc_final: 0.7856 (tt) REVERT: B 253 TYR cc_start: 0.7743 (m-80) cc_final: 0.7505 (m-80) REVERT: B 379 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7430 (tp30) REVERT: B 483 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8368 (m110) REVERT: C 253 TYR cc_start: 0.7949 (m-80) cc_final: 0.7658 (m-80) REVERT: C 280 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7020 (tm-30) REVERT: C 446 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8527 (p) REVERT: C 469 MET cc_start: 0.7903 (ttt) cc_final: 0.7689 (ttp) REVERT: C 636 MET cc_start: 0.8695 (mmp) cc_final: 0.8412 (mmm) outliers start: 25 outliers final: 17 residues processed: 185 average time/residue: 0.6797 time to fit residues: 186.5489 Evaluate side-chains 173 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 185 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 161 GLN B 534 ASN C 243 ASN C 526 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.136309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.104319 restraints weight = 50007.130| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.35 r_work: 0.3436 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15285 Z= 0.180 Angle : 0.494 6.056 20715 Z= 0.257 Chirality : 0.044 0.143 2142 Planarity : 0.004 0.048 2796 Dihedral : 4.349 18.429 2109 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.90 % Allowed : 10.58 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1869 helix: 2.21 (0.38), residues: 192 sheet: -0.99 (0.21), residues: 519 loop : -0.31 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 213 HIS 0.005 0.001 HIS C 499 PHE 0.015 0.001 PHE A 592 TYR 0.010 0.001 TYR B 497 ARG 0.010 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 155) hydrogen bonds : angle 4.01083 ( 348) covalent geometry : bond 0.00396 (15285) covalent geometry : angle 0.49355 (20715) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 2.345 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7533 (t0) cc_final: 0.7305 (p0) REVERT: A 153 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7450 (t0) REVERT: A 246 ARG cc_start: 0.8050 (mmt180) cc_final: 0.7172 (mmm160) REVERT: A 280 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7283 (tm-30) REVERT: A 519 ASP cc_start: 0.8125 (t0) cc_final: 0.7359 (m-30) REVERT: A 607 ARG cc_start: 0.5029 (ttt90) cc_final: 0.4190 (tpt90) REVERT: A 636 MET cc_start: 0.8827 (mmp) cc_final: 0.8552 (tpp) REVERT: B 46 LEU cc_start: 0.8430 (tp) cc_final: 0.8146 (tt) REVERT: B 253 TYR cc_start: 0.7786 (m-80) cc_final: 0.7530 (m-80) REVERT: B 379 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7461 (tp30) REVERT: B 483 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8377 (m110) REVERT: C 180 SER cc_start: 0.8224 (t) cc_final: 0.7855 (p) REVERT: C 253 TYR cc_start: 0.7937 (m-80) cc_final: 0.7638 (m-80) REVERT: C 280 GLN cc_start: 0.7859 (mm-40) cc_final: 0.6923 (tm-30) REVERT: C 446 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8484 (p) REVERT: C 469 MET cc_start: 0.7889 (ttt) cc_final: 0.7659 (ttp) REVERT: C 636 MET cc_start: 0.8706 (mmp) cc_final: 0.8424 (mmm) outliers start: 30 outliers final: 24 residues processed: 187 average time/residue: 0.5747 time to fit residues: 161.8921 Evaluate side-chains 185 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 74 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 159 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 148 optimal weight: 0.0970 chunk 68 optimal weight: 0.5980 chunk 153 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 112 GLN C 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.136938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.104759 restraints weight = 49820.089| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.36 r_work: 0.3438 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15285 Z= 0.128 Angle : 0.471 5.941 20715 Z= 0.244 Chirality : 0.044 0.157 2142 Planarity : 0.004 0.039 2796 Dihedral : 4.255 18.613 2109 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.65 % Allowed : 11.41 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1869 helix: 2.31 (0.38), residues: 192 sheet: -0.99 (0.21), residues: 519 loop : -0.29 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 96 HIS 0.004 0.001 HIS C 209 PHE 0.020 0.001 PHE B 33 TYR 0.008 0.001 TYR B 497 ARG 0.007 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 155) hydrogen bonds : angle 3.90400 ( 348) covalent geometry : bond 0.00284 (15285) covalent geometry : angle 0.47059 (20715) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 2.499 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7526 (t0) cc_final: 0.7308 (p0) REVERT: A 153 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7441 (t0) REVERT: A 246 ARG cc_start: 0.8069 (mmt180) cc_final: 0.7469 (mmp-170) REVERT: A 280 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7272 (tm-30) REVERT: A 519 ASP cc_start: 0.8205 (t0) cc_final: 0.7452 (m-30) REVERT: A 607 ARG cc_start: 0.5135 (ttt90) cc_final: 0.4215 (tpt90) REVERT: A 636 MET cc_start: 0.8821 (mmp) cc_final: 0.8544 (tpp) REVERT: B 253 TYR cc_start: 0.7768 (m-80) cc_final: 0.7521 (m-80) REVERT: B 379 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7493 (tp30) REVERT: C 180 SER cc_start: 0.8266 (t) cc_final: 0.7876 (p) REVERT: C 253 TYR cc_start: 0.7932 (m-80) cc_final: 0.7646 (m-80) REVERT: C 280 GLN cc_start: 0.7748 (mm-40) cc_final: 0.6845 (tm-30) REVERT: C 369 THR cc_start: 0.9235 (p) cc_final: 0.8903 (p) REVERT: C 446 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8486 (p) REVERT: C 469 MET cc_start: 0.7911 (ttt) cc_final: 0.7647 (ttp) REVERT: C 636 MET cc_start: 0.8694 (mmp) cc_final: 0.8474 (tpp) outliers start: 26 outliers final: 17 residues processed: 176 average time/residue: 0.5874 time to fit residues: 154.4835 Evaluate side-chains 175 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 518 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 90 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 129 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.139047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.107591 restraints weight = 50133.222| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.31 r_work: 0.3445 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15285 Z= 0.122 Angle : 0.463 5.950 20715 Z= 0.238 Chirality : 0.044 0.143 2142 Planarity : 0.003 0.034 2796 Dihedral : 4.132 18.207 2109 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.46 % Allowed : 11.66 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.19), residues: 1869 helix: 2.44 (0.38), residues: 192 sheet: -0.93 (0.22), residues: 519 loop : -0.27 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 96 HIS 0.003 0.001 HIS B 499 PHE 0.022 0.001 PHE B 33 TYR 0.008 0.001 TYR B 497 ARG 0.003 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 155) hydrogen bonds : angle 3.82507 ( 348) covalent geometry : bond 0.00274 (15285) covalent geometry : angle 0.46319 (20715) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 2.320 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7456 (t0) REVERT: A 519 ASP cc_start: 0.8094 (t0) cc_final: 0.7470 (m-30) REVERT: A 607 ARG cc_start: 0.5126 (ttt90) cc_final: 0.3658 (tpt90) REVERT: A 636 MET cc_start: 0.8806 (mmp) cc_final: 0.8532 (tpp) REVERT: B 27 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6826 (mm-30) REVERT: B 253 TYR cc_start: 0.7769 (m-80) cc_final: 0.7549 (m-80) REVERT: B 379 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: C 180 SER cc_start: 0.8296 (t) cc_final: 0.7945 (p) REVERT: C 253 TYR cc_start: 0.7903 (m-80) cc_final: 0.7637 (m-80) REVERT: C 280 GLN cc_start: 0.7756 (mm-40) cc_final: 0.6906 (tm-30) REVERT: C 369 THR cc_start: 0.9226 (p) cc_final: 0.8914 (p) REVERT: C 469 MET cc_start: 0.8095 (ttt) cc_final: 0.7799 (ttp) outliers start: 23 outliers final: 20 residues processed: 177 average time/residue: 0.6633 time to fit residues: 180.5222 Evaluate side-chains 175 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 518 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 167 optimal weight: 0.5980 chunk 165 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 112 GLN B 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.135177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.103802 restraints weight = 50412.783| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.35 r_work: 0.3426 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15285 Z= 0.143 Angle : 0.469 5.969 20715 Z= 0.242 Chirality : 0.043 0.142 2142 Planarity : 0.004 0.037 2796 Dihedral : 4.128 18.081 2109 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.39 % Allowed : 11.66 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1869 helix: 2.46 (0.39), residues: 192 sheet: -0.87 (0.22), residues: 480 loop : -0.41 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.004 0.001 HIS B 499 PHE 0.015 0.001 PHE B 33 TYR 0.008 0.001 TYR A 497 ARG 0.003 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 155) hydrogen bonds : angle 3.81137 ( 348) covalent geometry : bond 0.00317 (15285) covalent geometry : angle 0.46939 (20715) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 2.262 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7438 (t0) REVERT: A 519 ASP cc_start: 0.8101 (t0) cc_final: 0.7459 (m-30) REVERT: A 607 ARG cc_start: 0.4966 (ttt90) cc_final: 0.3569 (tpt90) REVERT: A 636 MET cc_start: 0.8820 (mmp) cc_final: 0.8555 (tpp) REVERT: B 253 TYR cc_start: 0.7791 (m-80) cc_final: 0.7528 (m-80) REVERT: B 379 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7537 (tp30) REVERT: C 180 SER cc_start: 0.8356 (t) cc_final: 0.7945 (p) REVERT: C 253 TYR cc_start: 0.7851 (m-80) cc_final: 0.7588 (m-80) REVERT: C 280 GLN cc_start: 0.7726 (mm-40) cc_final: 0.6888 (tm-30) REVERT: C 369 THR cc_start: 0.9229 (p) cc_final: 0.8918 (p) REVERT: C 469 MET cc_start: 0.8042 (ttt) cc_final: 0.7775 (ttp) REVERT: C 636 MET cc_start: 0.8742 (tpp) cc_final: 0.8506 (tpp) outliers start: 22 outliers final: 19 residues processed: 171 average time/residue: 0.5979 time to fit residues: 154.5959 Evaluate side-chains 176 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 518 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 25 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 164 optimal weight: 0.0970 chunk 103 optimal weight: 0.6980 chunk 121 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.136464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.104927 restraints weight = 50191.468| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.36 r_work: 0.3443 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15285 Z= 0.100 Angle : 0.454 5.911 20715 Z= 0.233 Chirality : 0.044 0.143 2142 Planarity : 0.003 0.033 2796 Dihedral : 3.998 17.899 2109 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.08 % Allowed : 12.17 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 1869 helix: 2.67 (0.39), residues: 192 sheet: -0.74 (0.22), residues: 480 loop : -0.37 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.005 0.001 HIS B 499 PHE 0.014 0.001 PHE B 33 TYR 0.006 0.001 TYR A 497 ARG 0.002 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 155) hydrogen bonds : angle 3.68583 ( 348) covalent geometry : bond 0.00229 (15285) covalent geometry : angle 0.45412 (20715) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 2.724 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7520 (t0) REVERT: A 246 ARG cc_start: 0.8207 (mmt180) cc_final: 0.7146 (mmm160) REVERT: A 280 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7133 (tm-30) REVERT: A 519 ASP cc_start: 0.8113 (t0) cc_final: 0.7490 (m-30) REVERT: A 555 SER cc_start: 0.8545 (t) cc_final: 0.8208 (m) REVERT: A 607 ARG cc_start: 0.5037 (ttt90) cc_final: 0.3626 (tpt90) REVERT: A 636 MET cc_start: 0.8821 (mmp) cc_final: 0.8560 (tpp) REVERT: B 62 LEU cc_start: 0.8294 (mt) cc_final: 0.8081 (tt) REVERT: B 379 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7626 (tp30) REVERT: C 180 SER cc_start: 0.8329 (t) cc_final: 0.7946 (p) REVERT: C 280 GLN cc_start: 0.7736 (mm-40) cc_final: 0.6909 (tm-30) REVERT: C 469 MET cc_start: 0.8127 (ttt) cc_final: 0.7871 (ttp) REVERT: C 636 MET cc_start: 0.8758 (tpp) cc_final: 0.8492 (tpp) outliers start: 17 outliers final: 14 residues processed: 175 average time/residue: 0.8171 time to fit residues: 221.2721 Evaluate side-chains 171 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 4.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 518 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 115 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 133 optimal weight: 0.2980 chunk 163 optimal weight: 1.9990 chunk 168 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 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 112 GLN B 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.135544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.104325 restraints weight = 50248.846| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.33 r_work: 0.3433 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15285 Z= 0.126 Angle : 0.465 5.910 20715 Z= 0.238 Chirality : 0.043 0.140 2142 Planarity : 0.003 0.036 2796 Dihedral : 4.010 17.473 2109 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.27 % Allowed : 12.10 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1869 helix: 2.67 (0.39), residues: 192 sheet: -0.75 (0.22), residues: 480 loop : -0.42 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.004 0.001 HIS B 499 PHE 0.015 0.001 PHE A 592 TYR 0.008 0.001 TYR C 253 ARG 0.002 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 155) hydrogen bonds : angle 3.68104 ( 348) covalent geometry : bond 0.00284 (15285) covalent geometry : angle 0.46548 (20715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15753.63 seconds wall clock time: 274 minutes 34.06 seconds (16474.06 seconds total)