Starting phenix.real_space_refine on Thu Feb 13 18:53:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ops_17086/02_2025/8ops_17086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ops_17086/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ops_17086/02_2025/8ops_17086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ops_17086/02_2025/8ops_17086.map" model { file = "/net/cci-nas-00/data/ceres_data/8ops_17086/02_2025/8ops_17086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ops_17086/02_2025/8ops_17086.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: 5.69, per 1000 atoms: 0.62 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: 2.75 Conformation dependent library (CDL) restraints added in 528.8 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: 4.10 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: 3.52 Time building geometry restraints manager: 3.11 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: 4.690 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: 0.160 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.930 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.950 ------------------------------------------------------------------------------- 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 5230 Z= 0.176 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.035 0.003 TRP A 509 HIS 0.013 0.002 HIS A 260 PHE 0.021 0.001 PHE A 469 TYR 0.009 0.001 TYR A 626 ARG 0.006 0.000 ARG A 316 *********************** 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 : 0.633 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: 0.4349 time to fit residues: 47.8336 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 : 0.879 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.4685 r_free = 0.4685 target = 0.190280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.165325 restraints weight = 35049.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.170885 restraints weight = 17520.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.174433 restraints weight = 10226.672| |-----------------------------------------------------------------------------| r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5384 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5230 Z= 0.202 Angle : 0.571 7.017 7421 Z= 0.303 Chirality : 0.039 0.210 898 Planarity : 0.006 0.046 692 Dihedral : 22.544 111.120 1544 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.08 % Allowed : 17.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.38), residues: 437 helix: 2.37 (0.37), residues: 191 sheet: -0.15 (0.77), residues: 43 loop : 0.02 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 509 HIS 0.007 0.002 HIS A 329 PHE 0.010 0.001 PHE A 440 TYR 0.017 0.002 TYR A 562 ARG 0.005 0.001 ARG A 337 *********************** 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: 8 poor density : 83 time to evaluate : 0.616 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 260 HIS cc_start: 0.5611 (m170) cc_final: 0.5388 (m170) REVERT: A 331 LEU cc_start: 0.6393 (mm) cc_final: 0.6060 (mm) REVERT: A 369 LEU cc_start: 0.7850 (mt) cc_final: 0.7453 (mt) REVERT: A 378 ASN cc_start: 0.5822 (p0) cc_final: 0.5603 (p0) REVERT: A 415 ASN cc_start: 0.8114 (m-40) cc_final: 0.7851 (t0) outliers start: 8 outliers final: 5 residues processed: 88 average time/residue: 0.4704 time to fit residues: 50.3463 Evaluate side-chains 85 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 37 optimal weight: 0.3980 chunk 23 optimal weight: 0.0770 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 14 optimal weight: 0.7980 overall best weight: 0.1494 ------------------------------------------------------------------------------- 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 = 0.4697 r_free = 0.4697 target = 0.191276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.166985 restraints weight = 36304.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.172311 restraints weight = 17971.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.175735 restraints weight = 10454.036| |-----------------------------------------------------------------------------| r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5349 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5230 Z= 0.130 Angle : 0.495 6.343 7421 Z= 0.260 Chirality : 0.036 0.217 898 Planarity : 0.004 0.045 692 Dihedral : 22.441 111.369 1544 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.08 % Allowed : 16.88 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.39), residues: 437 helix: 2.45 (0.37), residues: 197 sheet: -0.06 (0.75), residues: 44 loop : 0.11 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 509 HIS 0.006 0.001 HIS A 262 PHE 0.010 0.001 PHE A 462 TYR 0.007 0.001 TYR A 626 ARG 0.001 0.000 ARG A 441 *********************** 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 91 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LYS cc_start: 0.6763 (mmmm) cc_final: 0.6511 (mmmm) REVERT: A 369 LEU cc_start: 0.7710 (mt) cc_final: 0.7314 (mt) REVERT: A 415 ASN cc_start: 0.8132 (m-40) cc_final: 0.7840 (t0) outliers start: 8 outliers final: 6 residues processed: 85 average time/residue: 0.4900 time to fit residues: 49.9576 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 : 0.660 ------------------------------------------------------------------------------- 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 373 GLN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 382 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN A 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.182551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.157239 restraints weight = 35360.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.162600 restraints weight = 17996.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.166089 restraints weight = 10622.801| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5230 Z= 0.260 Angle : 0.610 7.929 7421 Z= 0.325 Chirality : 0.040 0.210 898 Planarity : 0.005 0.054 692 Dihedral : 22.586 111.195 1544 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.37), residues: 437 helix: 1.50 (0.36), residues: 190 sheet: -0.38 (0.75), residues: 43 loop : 0.08 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 509 HIS 0.021 0.003 HIS A 260 PHE 0.011 0.002 PHE B 163 TYR 0.010 0.002 TYR A 339 ARG 0.005 0.001 ARG A 223 *********************** 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: 6 poor density : 79 time to evaluate : 0.600 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 312 ASN cc_start: 0.8619 (m110) cc_final: 0.8323 (m110) REVERT: A 369 LEU cc_start: 0.7964 (mt) cc_final: 0.7587 (mt) REVERT: A 415 ASN cc_start: 0.8079 (m-40) cc_final: 0.7877 (t0) outliers start: 6 outliers final: 4 residues processed: 84 average time/residue: 0.5424 time to fit residues: 54.3195 Evaluate side-chains 81 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.0980 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 overall best weight: 0.3138 ------------------------------------------------------------------------------- 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 = 0.4630 r_free = 0.4630 target = 0.184405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.159256 restraints weight = 35462.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.164715 restraints weight = 17969.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.168247 restraints weight = 10585.763| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5641 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5230 Z= 0.145 Angle : 0.502 5.233 7421 Z= 0.266 Chirality : 0.036 0.226 898 Planarity : 0.004 0.044 692 Dihedral : 22.500 111.531 1544 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.39), residues: 437 helix: 1.98 (0.37), residues: 191 sheet: -0.09 (0.85), residues: 37 loop : 0.08 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 555 HIS 0.010 0.001 HIS A 260 PHE 0.016 0.001 PHE A 462 TYR 0.008 0.001 TYR A 626 ARG 0.002 0.000 ARG A 441 *********************** 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 81 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.655 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 312 ASN cc_start: 0.8609 (m110) cc_final: 0.8297 (m110) REVERT: A 327 PHE cc_start: 0.7592 (m-80) cc_final: 0.6974 (m-80) REVERT: A 369 LEU cc_start: 0.7962 (mt) cc_final: 0.7597 (mt) REVERT: A 374 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7358 (tm-30) outliers start: 7 outliers final: 4 residues processed: 77 average time/residue: 0.5133 time to fit residues: 47.1712 Evaluate side-chains 77 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN 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 12 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.177075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.151673 restraints weight = 34460.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.157007 restraints weight = 17504.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.160544 restraints weight = 10424.643| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5230 Z= 0.294 Angle : 0.607 6.104 7421 Z= 0.326 Chirality : 0.040 0.219 898 Planarity : 0.005 0.047 692 Dihedral : 22.706 111.446 1542 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.56 % Allowed : 20.52 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.39), residues: 437 helix: 1.47 (0.36), residues: 190 sheet: -0.32 (0.82), residues: 38 loop : -0.12 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 555 HIS 0.009 0.002 HIS A 262 PHE 0.016 0.002 PHE B 163 TYR 0.017 0.002 TYR A 562 ARG 0.005 0.001 ARG A 583 *********************** 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 83 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.619 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: 0.8071 (mt) cc_final: 0.7863 (mt) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.5555 time to fit residues: 52.3188 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 : 0.657 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.177599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.152270 restraints weight = 34813.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.157793 restraints weight = 17644.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.161262 restraints weight = 10376.980| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5230 Z= 0.198 Angle : 0.534 6.062 7421 Z= 0.286 Chirality : 0.037 0.235 898 Planarity : 0.004 0.045 692 Dihedral : 22.653 111.976 1542 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.82 % Allowed : 21.04 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.39), residues: 437 helix: 1.81 (0.37), residues: 190 sheet: -1.02 (0.67), residues: 47 loop : -0.27 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 555 HIS 0.007 0.001 HIS A 262 PHE 0.018 0.002 PHE A 462 TYR 0.011 0.002 TYR A 626 ARG 0.003 0.000 ARG A 226 *********************** 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 83 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.697 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: 0.8145 (mt) cc_final: 0.7941 (mt) outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 0.6025 time to fit residues: 55.8399 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 : 0.695 ------------------------------------------------------------------------------- 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 A residue 409 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 chunk 29 optimal weight: 0.0040 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.3170 ------------------------------------------------------------------------------- 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 = 0.179300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.153885 restraints weight = 35051.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.159460 restraints weight = 18033.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.163069 restraints weight = 10697.682| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5230 Z= 0.156 Angle : 0.500 6.543 7421 Z= 0.265 Chirality : 0.036 0.238 898 Planarity : 0.004 0.043 692 Dihedral : 22.473 111.014 1542 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.78 % Allowed : 22.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.40), residues: 437 helix: 2.18 (0.37), residues: 191 sheet: -1.14 (0.66), residues: 47 loop : -0.23 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 555 HIS 0.006 0.001 HIS A 262 PHE 0.017 0.002 PHE A 462 TYR 0.017 0.002 TYR A 626 ARG 0.004 0.000 ARG A 226 *********************** 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 75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.658 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 327 PHE cc_start: 0.7652 (m-80) cc_final: 0.7411 (m-80) outliers start: 3 outliers final: 3 residues processed: 74 average time/residue: 0.5261 time to fit residues: 46.3389 Evaluate side-chains 73 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 380 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4559 r_free = 0.4559 target = 0.178133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.152284 restraints weight = 34543.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.157887 restraints weight = 17705.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.161531 restraints weight = 10500.940| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5230 Z= 0.174 Angle : 0.511 6.342 7421 Z= 0.274 Chirality : 0.036 0.237 898 Planarity : 0.006 0.098 692 Dihedral : 22.469 110.939 1539 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.30 % Allowed : 23.64 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.40), residues: 437 helix: 2.28 (0.37), residues: 190 sheet: -1.25 (0.65), residues: 47 loop : -0.22 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 555 HIS 0.006 0.001 HIS A 262 PHE 0.019 0.002 PHE A 327 TYR 0.011 0.002 TYR A 562 ARG 0.010 0.001 ARG A 441 *********************** 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 75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.701 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 219 GLN cc_start: 0.6248 (tm-30) cc_final: 0.5300 (tt0) REVERT: A 327 PHE cc_start: 0.7714 (m-80) cc_final: 0.7495 (m-80) REVERT: A 591 LYS cc_start: 0.7535 (tptp) cc_final: 0.7307 (tptp) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.5472 time to fit residues: 47.4372 Evaluate side-chains 74 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4538 r_free = 0.4538 target = 0.176172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.150438 restraints weight = 34898.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.156019 restraints weight = 17763.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.159655 restraints weight = 10498.613| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5230 Z= 0.204 Angle : 0.538 6.405 7421 Z= 0.285 Chirality : 0.037 0.242 898 Planarity : 0.005 0.065 692 Dihedral : 22.587 110.590 1539 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.78 % Allowed : 24.42 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.40), residues: 437 helix: 2.16 (0.38), residues: 190 sheet: -1.32 (0.65), residues: 46 loop : -0.36 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 555 HIS 0.007 0.001 HIS A 262 PHE 0.015 0.002 PHE A 462 TYR 0.016 0.002 TYR A 626 ARG 0.009 0.001 ARG A 441 ********************** 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 80 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.677 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 327 PHE cc_start: 0.7623 (m-80) cc_final: 0.7377 (m-80) REVERT: A 560 ARG cc_start: 0.6932 (ttm170) cc_final: 0.6541 (ttt90) outliers start: 3 outliers final: 3 residues processed: 78 average time/residue: 0.5462 time to fit residues: 50.2082 Evaluate side-chains 77 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN 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 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4527 r_free = 0.4527 target = 0.174976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.149338 restraints weight = 34015.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.154900 restraints weight = 17430.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.158494 restraints weight = 10334.146| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5230 Z= 0.218 Angle : 0.550 6.299 7421 Z= 0.295 Chirality : 0.038 0.249 898 Planarity : 0.006 0.101 692 Dihedral : 22.637 110.967 1539 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.78 % Allowed : 24.68 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.40), residues: 437 helix: 2.09 (0.38), residues: 190 sheet: -1.41 (0.66), residues: 46 loop : -0.47 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 555 HIS 0.011 0.002 HIS A 260 PHE 0.018 0.002 PHE A 327 TYR 0.013 0.002 TYR A 626 ARG 0.009 0.001 ARG A 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4560.58 seconds wall clock time: 80 minutes 58.41 seconds (4858.41 seconds total)