Starting phenix.real_space_refine on Wed Aug 5 09:24:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ops_17086/08_2026/8ops_17086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ops_17086/08_2026/8ops_17086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ops_17086/08_2026/8ops_17086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ops_17086/08_2026/8ops_17086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ops_17086/08_2026/8ops_17086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ops_17086/08_2026/8ops_17086.map" } resolution = 3.82 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 69 5.49 5 S 19 5.16 5 C 2905 2.51 5 N 874 2.21 5 O 1115 1.98 5 H 4258 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9241 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6459 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 565 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 2216 Classifications: {'RNA': 69} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 25} Link IDs: {'rna2p': 12, 'rna3p': 56} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6508 SG CYS B 139 42.916 39.813 40.495 1.00130.08 S ATOM 6553 SG CYS B 142 46.905 37.913 39.572 1.00133.43 S ATOM 6674 SG CYS B 152 44.444 36.160 40.172 1.00129.36 S Time building chain proxies: 1.45, per 1000 atoms: 0.16 Number of scatterers: 9241 At special positions: 0 Unit cell: (79.05, 80.91, 134.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 19 16.00 P 69 15.00 O 1115 8.00 N 874 7.00 C 2905 6.00 H 4258 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: 0.55 Conformation dependent library (CDL) restraints added in 184.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 142 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 152 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 139 " 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 852 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 3 sheets defined 45.2% alpha, 8.3% beta 2 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 210 through 227 Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 265 through 283 Processing helix chain 'A' and resid 288 through 306 Processing helix chain 'A' and resid 309 through 329 removed outlier: 4.247A pdb=" N HIS A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.538A pdb=" N CYS A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 458 through 473 removed outlier: 3.995A pdb=" N PHE A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 463 " --> pdb=" O PRO A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 564 Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.664A pdb=" N LYS A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 630 Processing sheet with id=AA1, first strand: chain 'A' and resid 229 through 231 Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 338 removed outlier: 6.982A pdb=" N VAL A 397 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A 385 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 503 removed outlier: 7.047A pdb=" N ILE A 508 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE A 502 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4244 1.03 - 1.23: 36 1.23 - 1.42: 2335 1.42 - 1.62: 2852 1.62 - 1.81: 21 Bond restraints: 9488 Sorted by residual: bond pdb=" CB PRO A 287 " pdb=" CG PRO A 287 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 4.01e+00 bond pdb=" CA VAL A 434 " pdb=" CB VAL A 434 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.29e+00 bond pdb=" CA ASP B 137 " pdb=" CB ASP B 137 " ideal model delta sigma weight residual 1.532 1.550 -0.018 1.74e-02 3.30e+03 1.11e+00 bond pdb=" N9 A C 69 " pdb=" C4 A C 69 " ideal model delta sigma weight residual 1.374 1.380 -0.006 6.00e-03 2.78e+04 9.65e-01 bond pdb=" CA TRP A 509 " pdb=" CB TRP A 509 " ideal model delta sigma weight residual 1.535 1.554 -0.018 1.90e-02 2.77e+03 9.47e-01 ... (remaining 9483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 16659 1.81 - 3.62: 484 3.62 - 5.43: 23 5.43 - 7.23: 0 7.23 - 9.04: 1 Bond angle restraints: 17167 Sorted by residual: angle pdb=" O5' C C 30 " pdb=" C5' C C 30 " pdb=" C4' C C 30 " ideal model delta sigma weight residual 109.40 112.35 -2.95 8.00e-01 1.56e+00 1.36e+01 angle pdb=" CA PRO A 287 " pdb=" N PRO A 287 " pdb=" CD PRO A 287 " ideal model delta sigma weight residual 112.00 106.99 5.01 1.40e+00 5.10e-01 1.28e+01 angle pdb=" O5' G C 34 " pdb=" C5' G C 34 " pdb=" C4' G C 34 " ideal model delta sigma weight residual 109.40 112.26 -2.86 8.00e-01 1.56e+00 1.28e+01 angle pdb=" O5' G C 44 " pdb=" C5' G C 44 " pdb=" C4' G C 44 " ideal model delta sigma weight residual 109.40 112.07 -2.67 8.00e-01 1.56e+00 1.12e+01 angle pdb=" O5' C C 43 " pdb=" C5' C C 43 " pdb=" C4' C C 43 " ideal model delta sigma weight residual 109.40 112.07 -2.67 8.00e-01 1.56e+00 1.11e+01 ... (remaining 17162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 3943 21.77 - 43.54: 362 43.54 - 65.32: 206 65.32 - 87.09: 29 87.09 - 108.86: 4 Dihedral angle restraints: 4544 sinusoidal: 3040 harmonic: 1504 Sorted by residual: dihedral pdb=" O4' C C 30 " pdb=" C1' C C 30 " pdb=" N1 C C 30 " pdb=" C2 C C 30 " ideal model delta sinusoidal sigma weight residual -128.00 -61.59 -66.41 1 1.70e+01 3.46e-03 1.99e+01 dihedral pdb=" O4' C C 18 " pdb=" C1' C C 18 " pdb=" N1 C C 18 " pdb=" C2 C C 18 " ideal model delta sinusoidal sigma weight residual -128.00 -65.76 -62.24 1 1.70e+01 3.46e-03 1.77e+01 dihedral pdb=" O4' U C 36 " pdb=" C1' U C 36 " pdb=" N1 U C 36 " pdb=" C2 U C 36 " ideal model delta sinusoidal sigma weight residual -160.00 -106.72 -53.28 1 1.50e+01 4.44e-03 1.72e+01 ... (remaining 4541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 687 0.045 - 0.090: 116 0.090 - 0.136: 89 0.136 - 0.181: 5 0.181 - 0.226: 1 Chirality restraints: 898 Sorted by residual: chirality pdb=" C1' A C 69 " pdb=" O4' A C 69 " pdb=" C2' A C 69 " pdb=" N9 A C 69 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL A 385 " pdb=" CA VAL A 385 " pdb=" CG1 VAL A 385 " pdb=" CG2 VAL A 385 " both_signs ideal model delta sigma weight residual False -2.63 -2.79 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" C1' A C 62 " pdb=" O4' A C 62 " pdb=" C2' A C 62 " pdb=" N9 A C 62 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 895 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 286 " 0.063 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO A 287 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 509 " -0.014 2.00e-02 2.50e+03 1.04e-02 4.32e+00 pdb=" CG TRP A 509 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 509 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 509 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 509 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 509 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 509 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 509 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 509 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 509 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 509 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP A 509 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 509 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 509 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 509 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 509 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 157 " 0.035 5.00e-02 4.00e+02 5.16e-02 4.27e+00 pdb=" N PRO B 158 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 158 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 158 " 0.029 5.00e-02 4.00e+02 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 383 2.18 - 2.79: 17078 2.79 - 3.39: 25080 3.39 - 4.00: 32305 4.00 - 4.60: 48572 Nonbonded interactions: 123418 Sorted by model distance: nonbonded pdb=" O MET A 465 " pdb=" HH TYR A 562 " model vdw 1.577 2.450 nonbonded pdb=" OE1 GLN A 546 " pdb=" H GLN A 546 " model vdw 1.665 2.450 nonbonded pdb=" O CYS A 447 " pdb=" HG SER A 448 " model vdw 1.705 2.450 nonbonded pdb=" OE2 GLU A 318 " pdb="HH21 ARG A 321 " model vdw 1.734 2.450 nonbonded pdb=" HZ1 LYS A 445 " pdb=" OD2 ASP A 450 " model vdw 1.738 2.450 ... (remaining 123413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.040 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.390 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5006 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 5233 Z= 0.144 Angle : 0.650 9.044 7421 Z= 0.457 Chirality : 0.046 0.226 898 Planarity : 0.006 0.093 692 Dihedral : 21.448 108.861 2407 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.78 % Allowed : 18.70 % Favored : 80.52 % 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: 1.99 (0.39), residues: 437 helix: 2.78 (0.37), residues: 190 sheet: 0.03 (0.77), residues: 38 loop : 0.26 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 316 TYR 0.009 0.001 TYR A 626 PHE 0.021 0.001 PHE A 469 TRP 0.035 0.003 TRP A 509 HIS 0.013 0.002 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 5230) covalent geometry : angle 0.65046 / 0.46 ( 7421) hydrogen bonds : bond 0.12563 / 8.10 ( 174) hydrogen bonds : angle 5.82545 / 4.16 ( 500) metal coordination : bond 0.00681 / 0.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.145 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: A 275 LYS cc_start: 0.6727 (mmmm) cc_final: 0.6418 (mmmm) REVERT: A 415 ASN cc_start: 0.8104 (m-40) cc_final: 0.7789 (t0) outliers start: 3 outliers final: 2 residues processed: 89 average time/residue: 0.1482 time to fit residues: 16.6360 Evaluate side-chains 78 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 373 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 HIS ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.192226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.167709 restraints weight = 35916.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.173237 restraints weight = 17886.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.176629 restraints weight = 10401.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.178892 restraints weight = 6853.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.180448 restraints weight = 4979.719| |-----------------------------------------------------------------------------| r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5089 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5233 Z= 0.144 Angle : 0.538 7.667 7421 Z= 0.292 Chirality : 0.039 0.216 898 Planarity : 0.005 0.047 692 Dihedral : 22.442 108.820 1544 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.56 % Allowed : 18.18 % Favored : 80.26 % 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: 1.81 (0.39), residues: 437 helix: 2.53 (0.37), residues: 196 sheet: 0.07 (0.76), residues: 44 loop : 0.16 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 345 TYR 0.014 0.002 TYR A 562 PHE 0.011 0.001 PHE A 469 TRP 0.018 0.002 TRP A 509 HIS 0.006 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 5230) covalent geometry : angle 0.53773 / 0.29 ( 7421) hydrogen bonds : bond 0.05331 / 3.38 ( 174) hydrogen bonds : angle 5.17996 / 3.69 ( 500) metal coordination : bond 0.00174 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.219 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: A 369 LEU cc_start: 0.7803 (mt) cc_final: 0.7393 (mt) REVERT: A 374 GLU cc_start: 0.8020 (tp30) cc_final: 0.7734 (tp30) REVERT: A 415 ASN cc_start: 0.8123 (m-40) cc_final: 0.7842 (t0) outliers start: 6 outliers final: 5 residues processed: 84 average time/residue: 0.1828 time to fit residues: 18.9580 Evaluate side-chains 81 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 164 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.179886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.154647 restraints weight = 35674.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.160116 restraints weight = 17935.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.163582 restraints weight = 10554.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.165840 restraints weight = 6990.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.167394 restraints weight = 5109.819| |-----------------------------------------------------------------------------| r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5592 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 5233 Z= 0.281 Angle : 0.782 12.738 7421 Z= 0.424 Chirality : 0.046 0.279 898 Planarity : 0.006 0.050 692 Dihedral : 22.681 110.713 1544 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.64 % Allowed : 16.36 % Favored : 80.00 % 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: -0.03 (0.36), residues: 437 helix: 0.53 (0.34), residues: 196 sheet: -0.44 (0.73), residues: 43 loop : -0.34 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 583 TYR 0.019 0.004 TYR A 617 PHE 0.023 0.003 PHE B 163 TRP 0.011 0.004 TRP A 555 HIS 0.018 0.002 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.28 ( 5230) covalent geometry : angle 0.78200 / 0.42 ( 7421) hydrogen bonds : bond 0.06387 / 4.16 ( 174) hydrogen bonds : angle 5.60617 / 4.04 ( 500) metal coordination : bond 0.01188 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.129 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: A 260 HIS cc_start: 0.7350 (m170) cc_final: 0.6840 (m90) REVERT: A 309 HIS cc_start: 0.6878 (m-70) cc_final: 0.6676 (m-70) REVERT: A 369 LEU cc_start: 0.8009 (mt) cc_final: 0.7643 (mt) REVERT: A 415 ASN cc_start: 0.8043 (m-40) cc_final: 0.7807 (t0) REVERT: A 469 PHE cc_start: 0.4489 (t80) cc_final: 0.3397 (t80) outliers start: 14 outliers final: 8 residues processed: 92 average time/residue: 0.1991 time to fit residues: 22.2043 Evaluate side-chains 87 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain B residue 169 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 0.0040 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.0870 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.2970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 536 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.183734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.158707 restraints weight = 35770.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.164126 restraints weight = 17868.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.167658 restraints weight = 10554.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.169845 restraints weight = 7001.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.171333 restraints weight = 5138.359| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5233 Z= 0.117 Angle : 0.535 5.906 7421 Z= 0.291 Chirality : 0.038 0.180 898 Planarity : 0.005 0.041 692 Dihedral : 22.556 111.766 1544 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % 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: 1.03 (0.38), residues: 437 helix: 1.49 (0.36), residues: 196 sheet: 0.61 (0.88), residues: 27 loop : 0.02 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 316 TYR 0.007 0.001 TYR A 626 PHE 0.018 0.001 PHE A 462 TRP 0.010 0.001 TRP A 555 HIS 0.005 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 5230) covalent geometry : angle 0.53516 / 0.29 ( 7421) hydrogen bonds : bond 0.04735 / 3.09 ( 174) hydrogen bonds : angle 5.01699 / 3.64 ( 500) metal coordination : bond 0.01382 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.165 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: A 260 HIS cc_start: 0.6684 (m170) cc_final: 0.6471 (m170) REVERT: A 369 LEU cc_start: 0.7699 (mt) cc_final: 0.7337 (mt) REVERT: A 415 ASN cc_start: 0.7838 (m-40) cc_final: 0.7616 (t0) outliers start: 11 outliers final: 9 residues processed: 80 average time/residue: 0.1590 time to fit residues: 15.5378 Evaluate side-chains 80 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 538 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.0370 chunk 29 optimal weight: 0.0040 chunk 45 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 25 optimal weight: 0.6980 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.183931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.158914 restraints weight = 35584.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.164354 restraints weight = 17896.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.167784 restraints weight = 10608.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.169982 restraints weight = 7084.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.171491 restraints weight = 5217.096| |-----------------------------------------------------------------------------| r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5233 Z= 0.112 Angle : 0.505 6.347 7421 Z= 0.272 Chirality : 0.037 0.159 898 Planarity : 0.004 0.042 692 Dihedral : 22.467 111.946 1544 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.08 % Allowed : 18.96 % Favored : 78.96 % 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: 1.27 (0.39), residues: 437 helix: 1.80 (0.37), residues: 197 sheet: 0.50 (0.90), residues: 27 loop : 0.04 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 316 TYR 0.011 0.001 TYR A 562 PHE 0.015 0.001 PHE A 462 TRP 0.009 0.001 TRP A 555 HIS 0.007 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 5230) covalent geometry : angle 0.50466 / 0.27 ( 7421) hydrogen bonds : bond 0.04445 / 2.90 ( 174) hydrogen bonds : angle 4.81345 / 3.50 ( 500) metal coordination : bond 0.01151 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.225 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 260 HIS cc_start: 0.6762 (m170) cc_final: 0.6519 (m170) REVERT: A 327 PHE cc_start: 0.7361 (m-80) cc_final: 0.6781 (m-80) REVERT: A 369 LEU cc_start: 0.7749 (mt) cc_final: 0.7385 (mt) REVERT: A 415 ASN cc_start: 0.7886 (m-40) cc_final: 0.7663 (t0) outliers start: 8 outliers final: 5 residues processed: 80 average time/residue: 0.2327 time to fit residues: 22.4226 Evaluate side-chains 79 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 382 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 0.0060 chunk 32 optimal weight: 0.0060 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.0060 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.3428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.183709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.158587 restraints weight = 35331.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.163994 restraints weight = 17850.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.167496 restraints weight = 10523.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.169734 restraints weight = 6981.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.171188 restraints weight = 5112.226| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5233 Z= 0.112 Angle : 0.500 6.477 7421 Z= 0.269 Chirality : 0.037 0.154 898 Planarity : 0.004 0.043 692 Dihedral : 22.429 111.473 1542 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.56 % Allowed : 18.44 % Favored : 80.00 % 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: 1.36 (0.39), residues: 437 helix: 2.02 (0.37), residues: 191 sheet: 0.60 (0.91), residues: 27 loop : -0.01 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 226 TYR 0.012 0.001 TYR A 626 PHE 0.013 0.001 PHE A 462 TRP 0.008 0.001 TRP A 555 HIS 0.006 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 5230) covalent geometry : angle 0.50045 / 0.27 ( 7421) hydrogen bonds : bond 0.04361 / 2.83 ( 174) hydrogen bonds : angle 4.68138 / 3.41 ( 500) metal coordination : bond 0.00853 / 0.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.171 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 260 HIS cc_start: 0.6802 (m170) cc_final: 0.6546 (m170) REVERT: A 369 LEU cc_start: 0.7783 (mt) cc_final: 0.7425 (mt) outliers start: 6 outliers final: 6 residues processed: 75 average time/residue: 0.1909 time to fit residues: 16.9509 Evaluate side-chains 78 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.0870 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.183128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.157668 restraints weight = 35926.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.163112 restraints weight = 18334.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.166667 restraints weight = 10846.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.168936 restraints weight = 7193.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.170442 restraints weight = 5265.071| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5534 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5233 Z= 0.112 Angle : 0.489 6.652 7421 Z= 0.262 Chirality : 0.036 0.146 898 Planarity : 0.004 0.046 692 Dihedral : 22.362 111.100 1542 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.08 % Allowed : 18.18 % Favored : 79.74 % 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: 1.34 (0.39), residues: 437 helix: 2.14 (0.37), residues: 191 sheet: -0.28 (0.80), residues: 36 loop : -0.02 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 623 TYR 0.023 0.002 TYR A 626 PHE 0.015 0.002 PHE A 327 TRP 0.008 0.001 TRP A 555 HIS 0.008 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 5230) covalent geometry : angle 0.48899 / 0.26 ( 7421) hydrogen bonds : bond 0.04232 / 2.75 ( 174) hydrogen bonds : angle 4.58064 / 3.34 ( 500) metal coordination : bond 0.01475 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 HIS cc_start: 0.6893 (m170) cc_final: 0.6659 (m170) REVERT: A 369 LEU cc_start: 0.7830 (mt) cc_final: 0.7467 (mt) REVERT: A 623 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7798 (mtm-85) outliers start: 8 outliers final: 7 residues processed: 75 average time/residue: 0.2023 time to fit residues: 18.3742 Evaluate side-chains 76 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.181723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.156509 restraints weight = 34301.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.161995 restraints weight = 17358.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.165630 restraints weight = 10209.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.167896 restraints weight = 6690.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.169436 restraints weight = 4828.847| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5233 Z= 0.123 Angle : 0.498 6.694 7421 Z= 0.267 Chirality : 0.037 0.146 898 Planarity : 0.004 0.047 692 Dihedral : 22.364 110.900 1542 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.82 % Allowed : 19.22 % Favored : 78.96 % 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: 1.17 (0.40), residues: 437 helix: 2.10 (0.37), residues: 190 sheet: -0.73 (0.73), residues: 46 loop : -0.08 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 223 TYR 0.020 0.002 TYR A 626 PHE 0.038 0.002 PHE A 327 TRP 0.007 0.001 TRP A 555 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 5230) covalent geometry : angle 0.49781 / 0.27 ( 7421) hydrogen bonds : bond 0.04262 / 2.76 ( 174) hydrogen bonds : angle 4.58517 / 3.34 ( 500) metal coordination : bond 0.01328 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.195 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: A 260 HIS cc_start: 0.7006 (m170) cc_final: 0.6755 (m170) REVERT: A 369 LEU cc_start: 0.7872 (mt) cc_final: 0.7540 (mt) outliers start: 7 outliers final: 7 residues processed: 74 average time/residue: 0.1715 time to fit residues: 15.2818 Evaluate side-chains 76 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 5.9990 chunk 37 optimal weight: 0.0470 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.180943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.156035 restraints weight = 34525.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.161412 restraints weight = 17553.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.164970 restraints weight = 10350.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.167205 restraints weight = 6793.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.168658 restraints weight = 4913.304| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5606 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5233 Z= 0.120 Angle : 0.491 6.884 7421 Z= 0.263 Chirality : 0.036 0.142 898 Planarity : 0.004 0.045 692 Dihedral : 22.350 110.930 1542 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.82 % Allowed : 19.48 % Favored : 78.70 % 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: 1.37 (0.39), residues: 437 helix: 2.23 (0.37), residues: 190 sheet: -0.23 (0.77), residues: 37 loop : -0.07 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 623 TYR 0.014 0.001 TYR A 626 PHE 0.016 0.002 PHE A 327 TRP 0.007 0.001 TRP A 555 HIS 0.009 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 5230) covalent geometry : angle 0.49142 / 0.26 ( 7421) hydrogen bonds : bond 0.04210 / 2.73 ( 174) hydrogen bonds : angle 4.52954 / 3.30 ( 500) metal coordination : bond 0.01205 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.130 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: A 260 HIS cc_start: 0.7100 (m170) cc_final: 0.6830 (m170) REVERT: A 369 LEU cc_start: 0.7920 (mt) cc_final: 0.7609 (mt) outliers start: 7 outliers final: 7 residues processed: 75 average time/residue: 0.1803 time to fit residues: 16.2936 Evaluate side-chains 79 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 8 optimal weight: 0.3980 chunk 15 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.181888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.156637 restraints weight = 35336.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.162051 restraints weight = 18128.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.165647 restraints weight = 10788.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.167896 restraints weight = 7149.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.169420 restraints weight = 5210.173| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5233 Z= 0.103 Angle : 0.487 6.731 7421 Z= 0.258 Chirality : 0.036 0.143 898 Planarity : 0.004 0.047 692 Dihedral : 22.301 110.821 1542 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.56 % Allowed : 19.74 % Favored : 78.70 % 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: 1.43 (0.39), residues: 437 helix: 2.34 (0.37), residues: 191 sheet: -0.12 (0.78), residues: 37 loop : -0.13 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 226 TYR 0.018 0.001 TYR A 626 PHE 0.017 0.002 PHE A 327 TRP 0.009 0.001 TRP A 555 HIS 0.007 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 5230) covalent geometry : angle 0.48718 / 0.26 ( 7421) hydrogen bonds : bond 0.03991 / 2.59 ( 174) hydrogen bonds : angle 4.42361 / 3.22 ( 500) metal coordination : bond 0.00216 / 0.11 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue MET 170 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.187 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: A 260 HIS cc_start: 0.7070 (m170) cc_final: 0.6829 (m170) outliers start: 6 outliers final: 6 residues processed: 72 average time/residue: 0.2018 time to fit residues: 17.5174 Evaluate side-chains 75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.181033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.155881 restraints weight = 35316.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.161343 restraints weight = 18163.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.164842 restraints weight = 10780.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.167084 restraints weight = 7143.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.168576 restraints weight = 5212.525| |-----------------------------------------------------------------------------| r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5630 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 5233 Z= 0.118 Angle : 0.502 6.559 7421 Z= 0.265 Chirality : 0.036 0.140 898 Planarity : 0.004 0.046 692 Dihedral : 22.296 110.705 1542 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.82 % Allowed : 20.00 % Favored : 78.18 % 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: 1.42 (0.40), residues: 437 helix: 2.27 (0.37), residues: 190 sheet: -0.18 (0.79), residues: 37 loop : -0.04 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 226 TYR 0.015 0.001 TYR A 626 PHE 0.014 0.001 PHE A 462 TRP 0.008 0.001 TRP A 555 HIS 0.007 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 5230) covalent geometry : angle 0.50214 / 0.27 ( 7421) hydrogen bonds : bond 0.04113 / 2.71 ( 174) hydrogen bonds : angle 4.46793 / 3.24 ( 500) metal coordination : bond 0.00236 / 0.12 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2119.36 seconds wall clock time: 36 minutes 38.15 seconds (2198.15 seconds total)