Starting phenix.real_space_refine on Sat Aug 23 02:52:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ops_17086/08_2025/8ops_17086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ops_17086/08_2025/8ops_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_2025/8ops_17086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ops_17086/08_2025/8ops_17086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ops_17086/08_2025/8ops_17086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ops_17086/08_2025/8ops_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-2.0-5787/lib/python3.9/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: 2.25, per 1000 atoms: 0.24 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: 1.13 Conformation dependent library (CDL) restraints added in 190.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.62 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: 1.58 Time building geometry restraints manager: 1.49 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=" 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 bond pdb=" CG PRO B 158 " pdb=" CD PRO B 158 " ideal model delta sigma weight residual 1.503 1.472 0.031 3.40e-02 8.65e+02 8.11e-01 ... (remaining 9483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 16780 1.81 - 3.62: 363 3.62 - 5.43: 23 5.43 - 7.23: 0 7.23 - 9.04: 1 Bond angle restraints: 17167 Sorted by residual: 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=" CA LEU A 371 " pdb=" CB LEU A 371 " pdb=" CG LEU A 371 " ideal model delta sigma weight residual 116.30 125.34 -9.04 3.50e+00 8.16e-02 6.68e+00 angle pdb=" CA PRO B 158 " pdb=" N PRO B 158 " pdb=" CD PRO B 158 " ideal model delta sigma weight residual 112.00 108.48 3.52 1.40e+00 5.10e-01 6.34e+00 angle pdb=" C LEU A 370 " pdb=" N LEU A 371 " pdb=" CA LEU A 371 " ideal model delta sigma weight residual 120.31 116.53 3.78 1.52e+00 4.33e-01 6.18e+00 angle pdb=" C2' A C 69 " pdb=" C1' A C 69 " pdb=" N9 A C 69 " ideal model delta sigma weight residual 112.00 115.54 -3.54 1.50e+00 4.44e-01 5.57e+00 ... (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 - 0.043: 739 0.043 - 0.085: 113 0.085 - 0.128: 37 0.128 - 0.170: 8 0.170 - 0.213: 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 2.46 2.25 0.21 2.00e-01 2.50e+01 1.13e+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=" CB VAL A 556 " pdb=" CA VAL A 556 " pdb=" CG1 VAL A 556 " pdb=" CG2 VAL A 556 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.65e-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: 4.170 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: 0.080 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.140 Find NCS groups from input model: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5130 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= 0.117 Angle : 0.568 9.044 7421 Z= 0.301 Chirality : 0.038 0.213 898 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 aren 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 covalent geometry : bond 0.00275 ( 5230) covalent geometry : angle 0.56831 ( 7421) hydrogen bonds : bond 0.12563 ( 174) hydrogen bonds : angle 5.82545 ( 500) metal coordination : bond 0.00681 ( 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 : 0.282 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: 0.1784 time to fit residues: 19.6256 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 : 0.185 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 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: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4691 r_free = 0.4691 target = 0.190944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.166089 restraints weight = 35880.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.171712 restraints weight = 17991.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.175176 restraints weight = 10523.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.177440 restraints weight = 6930.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.178738 restraints weight = 5031.921| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5290 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5233 Z= 0.137 Angle : 0.552 7.178 7421 Z= 0.293 Chirality : 0.038 0.210 898 Planarity : 0.005 0.046 692 Dihedral : 22.539 110.896 1544 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.34 % Allowed : 16.88 % Favored : 80.78 % 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 aren not related in a simple way. whole: 1.63 (0.39), residues: 437 helix: 2.37 (0.37), residues: 197 sheet: -0.03 (0.76), residues: 44 loop : 0.07 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 337 TYR 0.014 0.002 TYR A 562 PHE 0.010 0.001 PHE A 440 TRP 0.016 0.002 TRP A 509 HIS 0.006 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5230) covalent geometry : angle 0.55235 ( 7421) hydrogen bonds : bond 0.04304 ( 174) hydrogen bonds : angle 4.94872 ( 500) metal coordination : bond 0.00272 ( 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 91 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.143 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: 0.7797 (mt) cc_final: 0.7396 (mt) REVERT: A 378 ASN cc_start: 0.5819 (p0) cc_final: 0.5601 (p0) REVERT: A 415 ASN cc_start: 0.8094 (m-40) cc_final: 0.7823 (t0) outliers start: 9 outliers final: 5 residues processed: 87 average time/residue: 0.1914 time to fit residues: 19.8698 Evaluate side-chains 86 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 380 ASP 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: 2.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.0270 chunk 40 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A 329 HIS A 354 ASN A 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.182546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.157395 restraints weight = 35710.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.162828 restraints weight = 17918.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.166345 restraints weight = 10554.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.168590 restraints weight = 6981.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.170051 restraints weight = 5099.805| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5233 Z= 0.174 Angle : 0.581 5.242 7421 Z= 0.313 Chirality : 0.039 0.205 898 Planarity : 0.005 0.049 692 Dihedral : 22.619 111.826 1544 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.56 % Allowed : 17.14 % Favored : 81.30 % 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 aren not related in a simple way. whole: 1.24 (0.38), residues: 437 helix: 1.81 (0.37), residues: 196 sheet: -0.30 (0.75), residues: 43 loop : 0.18 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 223 TYR 0.010 0.002 TYR B 140 PHE 0.010 0.001 PHE B 163 TRP 0.008 0.002 TRP A 509 HIS 0.016 0.003 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 5230) covalent geometry : angle 0.58062 ( 7421) hydrogen bonds : bond 0.05175 ( 174) hydrogen bonds : angle 4.94721 ( 500) metal coordination : bond 0.00793 ( 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 83 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 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 369 LEU cc_start: 0.7819 (mt) cc_final: 0.7460 (mt) REVERT: A 374 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7493 (tm-30) REVERT: A 415 ASN cc_start: 0.8021 (m-40) cc_final: 0.7807 (t0) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.2355 time to fit residues: 22.8976 Evaluate side-chains 79 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.182272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.157322 restraints weight = 35541.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.162738 restraints weight = 17898.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.166245 restraints weight = 10541.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.168446 restraints weight = 6966.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.169939 restraints weight = 5086.987| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5625 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5233 Z= 0.128 Angle : 0.512 5.470 7421 Z= 0.274 Chirality : 0.037 0.226 898 Planarity : 0.004 0.047 692 Dihedral : 22.581 112.023 1542 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.86 % Allowed : 17.40 % 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 aren not related in a simple way. whole: 1.37 (0.39), residues: 437 helix: 2.14 (0.37), residues: 191 sheet: -0.21 (0.84), residues: 37 loop : 0.02 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 223 TYR 0.010 0.002 TYR A 626 PHE 0.014 0.001 PHE A 462 TRP 0.009 0.001 TRP A 555 HIS 0.010 0.002 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5230) covalent geometry : angle 0.51240 ( 7421) hydrogen bonds : bond 0.04194 ( 174) hydrogen bonds : angle 4.67763 ( 500) metal coordination : bond 0.00274 ( 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 86 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.229 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: A 369 LEU cc_start: 0.7862 (mt) cc_final: 0.7516 (mt) REVERT: A 374 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7477 (tm-30) outliers start: 11 outliers final: 7 residues processed: 80 average time/residue: 0.2447 time to fit residues: 23.0769 Evaluate side-chains 80 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.178430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.153169 restraints weight = 34651.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.158571 restraints weight = 17575.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.162149 restraints weight = 10491.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.164376 restraints weight = 6976.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.165890 restraints weight = 5105.055| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5233 Z= 0.150 Angle : 0.540 6.340 7421 Z= 0.287 Chirality : 0.038 0.220 898 Planarity : 0.005 0.048 692 Dihedral : 22.587 111.287 1542 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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 aren not related in a simple way. whole: 1.17 (0.40), residues: 437 helix: 2.00 (0.37), residues: 196 sheet: -0.75 (0.72), residues: 47 loop : -0.02 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 223 TYR 0.022 0.002 TYR A 626 PHE 0.016 0.002 PHE A 462 TRP 0.009 0.002 TRP A 555 HIS 0.010 0.002 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5230) covalent geometry : angle 0.53966 ( 7421) hydrogen bonds : bond 0.04353 ( 174) hydrogen bonds : angle 4.62162 ( 500) metal coordination : bond 0.01675 ( 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 83 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.216 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 312 ASN cc_start: 0.8526 (m110) cc_final: 0.8276 (m110) REVERT: A 316 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7993 (ttm170) REVERT: A 369 LEU cc_start: 0.7993 (mt) cc_final: 0.7792 (mt) REVERT: A 626 TYR cc_start: 0.5812 (t80) cc_final: 0.5574 (t80) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.2478 time to fit residues: 23.2775 Evaluate side-chains 77 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 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: 0.0970 chunk 32 optimal weight: 0.2980 chunk 4 optimal weight: 6.9990 chunk 29 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.180950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.156008 restraints weight = 34836.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.161517 restraints weight = 17677.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.165134 restraints weight = 10442.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.167360 restraints weight = 6848.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.168850 restraints weight = 4984.914| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5725 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5233 Z= 0.098 Angle : 0.482 5.825 7421 Z= 0.254 Chirality : 0.036 0.236 898 Planarity : 0.004 0.043 692 Dihedral : 22.455 111.334 1542 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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 aren not related in a simple way. whole: 1.41 (0.40), residues: 437 helix: 2.48 (0.37), residues: 191 sheet: -0.80 (0.70), residues: 47 loop : -0.12 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.010 0.001 TYR A 626 PHE 0.016 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 covalent geometry : bond 0.00207 ( 5230) covalent geometry : angle 0.48208 ( 7421) hydrogen bonds : bond 0.03825 ( 174) hydrogen bonds : angle 4.35224 ( 500) metal coordination : bond 0.00424 ( 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 77 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ASN cc_start: 0.8592 (m110) cc_final: 0.8378 (m110) outliers start: 6 outliers final: 5 residues processed: 73 average time/residue: 0.2417 time to fit residues: 20.4803 Evaluate side-chains 75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU 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 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: 0.0970 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.179184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.153749 restraints weight = 34946.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.159316 restraints weight = 17926.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.162922 restraints weight = 10625.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.165195 restraints weight = 7012.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.166491 restraints weight = 5101.826| |-----------------------------------------------------------------------------| r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 moved from start: 0.5150 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= 0.118 Angle : 0.493 6.140 7421 Z= 0.263 Chirality : 0.036 0.229 898 Planarity : 0.005 0.044 692 Dihedral : 22.444 111.026 1539 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.82 % Allowed : 21.30 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.40), residues: 437 helix: 2.53 (0.37), residues: 190 sheet: -0.95 (0.68), residues: 47 loop : -0.05 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 623 TYR 0.012 0.001 TYR A 562 PHE 0.022 0.001 PHE A 327 TRP 0.009 0.001 TRP A 555 HIS 0.009 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5230) covalent geometry : angle 0.49324 ( 7421) hydrogen bonds : bond 0.04017 ( 174) hydrogen bonds : angle 4.34756 ( 500) metal coordination : bond 0.00259 ( 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 77 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 TYR cc_start: 0.5683 (t80) cc_final: 0.5440 (t80) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.2323 time to fit residues: 20.1180 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 : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU 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 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: 6.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.0370 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.176968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.151138 restraints weight = 34870.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.156700 restraints weight = 17924.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.160291 restraints weight = 10649.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.162621 restraints weight = 7070.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.163907 restraints weight = 5162.198| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5233 Z= 0.143 Angle : 0.528 6.683 7421 Z= 0.284 Chirality : 0.037 0.231 898 Planarity : 0.006 0.112 692 Dihedral : 22.522 110.930 1539 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.82 % Allowed : 21.56 % Favored : 76.62 % 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 aren not related in a simple way. whole: 1.18 (0.40), residues: 437 helix: 2.24 (0.37), residues: 190 sheet: -1.06 (0.66), residues: 47 loop : -0.13 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 441 TYR 0.014 0.002 TYR A 562 PHE 0.029 0.002 PHE A 327 TRP 0.008 0.002 TRP A 555 HIS 0.008 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 5230) covalent geometry : angle 0.52801 ( 7421) hydrogen bonds : bond 0.04220 ( 174) hydrogen bonds : angle 4.50334 ( 500) metal coordination : bond 0.00264 ( 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 77 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 TYR cc_start: 0.5679 (t80) cc_final: 0.5446 (t80) outliers start: 7 outliers final: 7 residues processed: 73 average time/residue: 0.2277 time to fit residues: 19.6990 Evaluate side-chains 74 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU 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 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain B residue 164 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.178027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.152364 restraints weight = 35025.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.157932 restraints weight = 17795.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.161569 restraints weight = 10531.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.163868 restraints weight = 6941.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.165349 restraints weight = 5062.362| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5233 Z= 0.122 Angle : 0.511 6.216 7421 Z= 0.272 Chirality : 0.036 0.238 898 Planarity : 0.005 0.067 692 Dihedral : 22.474 110.893 1539 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.82 % Allowed : 21.82 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.40), residues: 437 helix: 2.37 (0.37), residues: 190 sheet: -1.16 (0.67), residues: 46 loop : -0.12 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 441 TYR 0.010 0.001 TYR A 626 PHE 0.017 0.001 PHE A 327 TRP 0.010 0.002 TRP A 555 HIS 0.007 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5230) covalent geometry : angle 0.51095 ( 7421) hydrogen bonds : bond 0.03959 ( 174) hydrogen bonds : angle 4.35719 ( 500) metal coordination : bond 0.00185 ( 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 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 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLN cc_start: 0.6243 (tm-30) cc_final: 0.5424 (tt0) REVERT: A 626 TYR cc_start: 0.5714 (t80) cc_final: 0.5424 (t80) outliers start: 7 outliers final: 6 residues processed: 72 average time/residue: 0.2200 time to fit residues: 18.8989 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 : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU 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 380 ASP Chi-restraints excluded: chain B residue 164 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 8 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 overall best weight: 0.1758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.179691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.154279 restraints weight = 35125.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.159755 restraints weight = 17813.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.163389 restraints weight = 10557.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.165691 restraints weight = 7000.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.167182 restraints weight = 5105.808| |-----------------------------------------------------------------------------| r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5233 Z= 0.098 Angle : 0.489 6.546 7421 Z= 0.259 Chirality : 0.035 0.240 898 Planarity : 0.006 0.092 692 Dihedral : 22.346 110.661 1539 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.30 % Allowed : 22.08 % Favored : 76.62 % 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 aren not related in a simple way. whole: 1.49 (0.40), residues: 437 helix: 2.64 (0.38), residues: 191 sheet: -1.10 (0.66), residues: 47 loop : -0.08 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 441 TYR 0.010 0.001 TYR A 626 PHE 0.015 0.001 PHE A 327 TRP 0.011 0.001 TRP A 555 HIS 0.008 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 5230) covalent geometry : angle 0.48920 ( 7421) hydrogen bonds : bond 0.03734 ( 174) hydrogen bonds : angle 4.17901 ( 500) metal coordination : bond 0.00219 ( 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 75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8420 (tpt) cc_final: 0.8144 (tpt) REVERT: A 327 PHE cc_start: 0.7677 (m-80) cc_final: 0.7367 (m-80) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.2175 time to fit residues: 18.3483 Evaluate side-chains 73 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 164 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.177987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.152527 restraints weight = 34901.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.157991 restraints weight = 17799.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.161609 restraints weight = 10570.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.163893 restraints weight = 7018.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.165391 restraints weight = 5134.082| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5878 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5233 Z= 0.117 Angle : 0.503 6.200 7421 Z= 0.267 Chirality : 0.036 0.234 898 Planarity : 0.005 0.079 692 Dihedral : 22.397 110.283 1539 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.30 % Allowed : 22.60 % Favored : 76.10 % 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 aren not related in a simple way. whole: 1.42 (0.40), residues: 437 helix: 2.57 (0.37), residues: 190 sheet: -1.10 (0.69), residues: 46 loop : -0.12 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 226 TYR 0.010 0.001 TYR A 599 PHE 0.015 0.001 PHE A 327 TRP 0.009 0.001 TRP A 555 HIS 0.007 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5230) covalent geometry : angle 0.50256 ( 7421) hydrogen bonds : bond 0.03851 ( 174) hydrogen bonds : angle 4.26736 ( 500) metal coordination : bond 0.00358 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2368.38 seconds wall clock time: 40 minutes 52.80 seconds (2452.80 seconds total)