Starting phenix.real_space_refine on Fri Aug 22 17:27:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rld_19339/08_2025/8rld_19339_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rld_19339/08_2025/8rld_19339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rld_19339/08_2025/8rld_19339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rld_19339/08_2025/8rld_19339.map" model { file = "/net/cci-nas-00/data/ceres_data/8rld_19339/08_2025/8rld_19339_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rld_19339/08_2025/8rld_19339_trim.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 17 5.16 5 C 2107 2.51 5 N 524 2.21 5 O 559 1.98 5 H 3209 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 6416 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6392 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.02, per 1000 atoms: 0.16 Number of scatterers: 6416 At special positions: 0 Unit cell: (54.988, 68.968, 81.084, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 O 559 8.00 N 524 7.00 C 2107 6.00 H 3209 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 203.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 93.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 100 through 125 removed outlier: 4.533A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 136 through 163 removed outlier: 3.684A pdb=" N LEU A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 166 through 187 Processing helix chain 'A' and resid 193 through 222 Proline residue: A 215 - end of helix removed outlier: 3.600A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 257 removed outlier: 4.460A pdb=" N LEU A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 259 through 281 removed outlier: 3.760A pdb=" N LEU A 263 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.647A pdb=" N ILE A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 312 through 347 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 360 through 390 removed outlier: 3.898A pdb=" N LEU A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 4.323A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 451 removed outlier: 3.577A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 474 through 490 Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 525 removed outlier: 4.358A pdb=" N PHE A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 539 removed outlier: 3.864A pdb=" N ASP A 529 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 539 " --> pdb=" O GLN A 535 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.59 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: 3201 1.03 - 1.23: 8 1.23 - 1.42: 1391 1.42 - 1.62: 1864 1.62 - 1.81: 26 Bond restraints: 6490 Sorted by residual: bond pdb=" C3' LMT A 601 " pdb=" O3' LMT A 601 " ideal model delta sigma weight residual 1.404 1.363 0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C7 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 1.529 1.489 0.040 2.00e-02 2.50e+03 3.93e+00 bond pdb=" C6' LMT A 601 " pdb=" O6' LMT A 601 " ideal model delta sigma weight residual 1.407 1.370 0.037 2.00e-02 2.50e+03 3.43e+00 bond pdb=" C2 LMT A 601 " pdb=" C3 LMT A 601 " ideal model delta sigma weight residual 1.529 1.493 0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C8 LMT A 601 " pdb=" C9 LMT A 601 " ideal model delta sigma weight residual 1.531 1.496 0.035 2.00e-02 2.50e+03 3.09e+00 ... (remaining 6485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 11584 1.98 - 3.96: 76 3.96 - 5.94: 15 5.94 - 7.92: 1 7.92 - 9.90: 2 Bond angle restraints: 11678 Sorted by residual: angle pdb=" C2 LMT A 601 " pdb=" C3 LMT A 601 " pdb=" C4 LMT A 601 " ideal model delta sigma weight residual 117.09 107.19 9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " pdb=" CG TRP A 178 " ideal model delta sigma weight residual 113.60 119.32 -5.72 1.90e+00 2.77e-01 9.07e+00 angle pdb=" C10 LMT A 601 " pdb=" C9 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 116.03 107.71 8.32 3.00e+00 1.11e-01 7.68e+00 angle pdb=" N TRP A 178 " pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " ideal model delta sigma weight residual 110.30 114.54 -4.24 1.54e+00 4.22e-01 7.59e+00 angle pdb=" C6 LMT A 601 " pdb=" C7 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 117.26 109.35 7.91 3.00e+00 1.11e-01 6.95e+00 ... (remaining 11673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 2772 16.00 - 32.00: 199 32.00 - 48.00: 43 48.00 - 64.01: 67 64.01 - 80.01: 2 Dihedral angle restraints: 3083 sinusoidal: 1617 harmonic: 1466 Sorted by residual: dihedral pdb=" CA THR A 392 " pdb=" C THR A 392 " pdb=" N GLN A 393 " pdb=" CA GLN A 393 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CG ARG A 342 " pdb=" CD ARG A 342 " pdb=" NE ARG A 342 " pdb=" CZ ARG A 342 " ideal model delta sinusoidal sigma weight residual -180.00 -137.42 -42.58 2 1.50e+01 4.44e-03 9.76e+00 dihedral pdb=" N LYS A 361 " pdb=" CA LYS A 361 " pdb=" CB LYS A 361 " pdb=" CG LYS A 361 " ideal model delta sinusoidal sigma weight residual -60.00 -112.13 52.13 3 1.50e+01 4.44e-03 9.08e+00 ... (remaining 3080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 424 0.044 - 0.088: 93 0.088 - 0.132: 10 0.132 - 0.176: 1 0.176 - 0.220: 3 Chirality restraints: 531 Sorted by residual: chirality pdb=" CB ILE A 247 " pdb=" CA ILE A 247 " pdb=" CG1 ILE A 247 " pdb=" CG2 ILE A 247 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C4' LMT A 601 " pdb=" C3' LMT A 601 " pdb=" C5' LMT A 601 " pdb=" O1B LMT A 601 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C5' LMT A 601 " pdb=" C4' LMT A 601 " pdb=" C6' LMT A 601 " pdb=" O5' LMT A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.31 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 528 not shown) Planarity restraints: 951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.022 2.00e-02 2.50e+03 1.33e-02 7.03e+00 pdb=" CG TRP A 178 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP A 178 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 178 " 0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 178 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 387 " 0.014 2.00e-02 2.50e+03 1.30e-02 6.81e+00 pdb=" CG TRP A 387 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A 387 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 387 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 387 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 387 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 387 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 387 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 387 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 387 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP A 387 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP A 387 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 387 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 387 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 387 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 387 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 228 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C THR A 228 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 228 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 229 " 0.012 2.00e-02 2.50e+03 ... (remaining 948 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 222 2.15 - 2.76: 12291 2.76 - 3.37: 19734 3.37 - 3.99: 24093 3.99 - 4.60: 38095 Nonbonded interactions: 94435 Sorted by model distance: nonbonded pdb=" O GLY A 206 " pdb=" HG SER A 209 " model vdw 1.535 2.450 nonbonded pdb=" O SER A 186 " pdb=" HD1 HIS A 260 " model vdw 1.652 2.450 nonbonded pdb=" O LEU A 161 " pdb=" H PHE A 165 " model vdw 1.680 2.450 nonbonded pdb=" O SER A 319 " pdb=" HG SER A 323 " model vdw 1.691 2.450 nonbonded pdb="HH12 ARG A 227 " pdb=" OG1 THR A 228 " model vdw 1.719 2.450 ... (remaining 94430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.880 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 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 0.041 3281 Z= 0.167 Angle : 0.595 9.898 4462 Z= 0.298 Chirality : 0.039 0.220 531 Planarity : 0.004 0.046 545 Dihedral : 12.393 80.008 1130 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.40), residues: 416 helix: 1.07 (0.26), residues: 371 sheet: None (None), residues: 0 loop : -0.34 (1.01), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.009 0.001 TYR A 160 PHE 0.009 0.001 PHE A 236 TRP 0.044 0.003 TRP A 387 HIS 0.001 0.000 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3281) covalent geometry : angle 0.59477 ( 4462) hydrogen bonds : bond 0.09968 ( 284) hydrogen bonds : angle 5.11372 ( 852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.4802 time to fit residues: 25.4425 Evaluate side-chains 44 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4419 r_free = 0.4419 target = 0.223475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.212657 restraints weight = 10873.833| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 1.43 r_work: 0.4305 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4212 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3281 Z= 0.162 Angle : 0.526 5.160 4462 Z= 0.287 Chirality : 0.036 0.129 531 Planarity : 0.005 0.050 545 Dihedral : 5.891 57.479 486 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.22 % Allowed : 8.23 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.87 (0.40), residues: 416 helix: 1.48 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.68 (0.97), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 200 TYR 0.010 0.001 TYR A 116 PHE 0.008 0.001 PHE A 151 TRP 0.022 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3281) covalent geometry : angle 0.52641 ( 4462) hydrogen bonds : bond 0.05655 ( 284) hydrogen bonds : angle 4.41529 ( 852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.7070 (mtt) cc_final: 0.5863 (tmm) outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 0.6078 time to fit residues: 39.5104 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.0270 chunk 17 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.215447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.205132 restraints weight = 10965.389| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 1.40 r_work: 0.4205 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.4109 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3281 Z= 0.197 Angle : 0.563 5.263 4462 Z= 0.315 Chirality : 0.037 0.124 531 Planarity : 0.005 0.048 545 Dihedral : 5.453 43.341 486 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.52 % Allowed : 11.59 % Favored : 86.89 % 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: 1.59 (0.39), residues: 416 helix: 1.37 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -1.11 (0.86), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 456 TYR 0.011 0.002 TYR A 116 PHE 0.011 0.002 PHE A 193 TRP 0.018 0.002 TRP A 178 HIS 0.005 0.002 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 3281) covalent geometry : angle 0.56264 ( 4462) hydrogen bonds : bond 0.06275 ( 284) hydrogen bonds : angle 4.62303 ( 852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.7084 (mtt) cc_final: 0.5940 (tmm) REVERT: A 334 MET cc_start: 0.8044 (ttt) cc_final: 0.7710 (tpt) REVERT: A 391 LYS cc_start: 0.7252 (mtpt) cc_final: 0.7024 (mtpm) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 0.5979 time to fit residues: 37.6991 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.0050 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.0770 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 overall best weight: 0.3550 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.220863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.211548 restraints weight = 10877.887| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 1.27 r_work: 0.4234 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.4150 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3281 Z= 0.144 Angle : 0.500 4.368 4462 Z= 0.277 Chirality : 0.035 0.127 531 Planarity : 0.005 0.039 545 Dihedral : 4.478 32.016 486 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.22 % Allowed : 14.63 % Favored : 84.15 % 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: 2.09 (0.40), residues: 416 helix: 1.70 (0.26), residues: 370 sheet: None (None), residues: 0 loop : -1.06 (0.88), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 532 TYR 0.010 0.001 TYR A 116 PHE 0.008 0.001 PHE A 327 TRP 0.019 0.002 TRP A 178 HIS 0.002 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3281) covalent geometry : angle 0.49964 ( 4462) hydrogen bonds : bond 0.05429 ( 284) hydrogen bonds : angle 4.32801 ( 852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: A 306 MET cc_start: 0.7051 (mtt) cc_final: 0.5886 (tmm) REVERT: A 334 MET cc_start: 0.7951 (ttt) cc_final: 0.7714 (tpt) REVERT: A 391 LYS cc_start: 0.7216 (mtpt) cc_final: 0.6964 (mtpm) REVERT: A 477 TYR cc_start: 0.8261 (t80) cc_final: 0.7953 (t80) outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 0.5850 time to fit residues: 34.9902 Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 9 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 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 = 0.4358 r_free = 0.4358 target = 0.217697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.208108 restraints weight = 11020.140| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 1.30 r_work: 0.4210 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.4124 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3281 Z= 0.176 Angle : 0.525 4.438 4462 Z= 0.296 Chirality : 0.036 0.128 531 Planarity : 0.005 0.046 545 Dihedral : 4.524 31.694 486 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.52 % Allowed : 14.33 % Favored : 84.15 % 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: 1.85 (0.40), residues: 416 helix: 1.55 (0.26), residues: 370 sheet: None (None), residues: 0 loop : -1.11 (0.88), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.011 0.001 TYR A 116 PHE 0.008 0.001 PHE A 151 TRP 0.020 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3281) covalent geometry : angle 0.52544 ( 4462) hydrogen bonds : bond 0.05909 ( 284) hydrogen bonds : angle 4.47597 ( 852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 306 MET cc_start: 0.7075 (mtt) cc_final: 0.5917 (tmm) REVERT: A 334 MET cc_start: 0.7995 (ttt) cc_final: 0.7788 (tpt) REVERT: A 391 LYS cc_start: 0.7284 (mtpt) cc_final: 0.7063 (mtpm) outliers start: 5 outliers final: 4 residues processed: 59 average time/residue: 0.5863 time to fit residues: 36.2909 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 0.0770 chunk 21 optimal weight: 0.3980 chunk 3 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 overall best weight: 0.2936 ------------------------------------------------------------------------------- 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 = 0.4385 r_free = 0.4385 target = 0.220912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.211207 restraints weight = 10956.924| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 1.33 r_work: 0.4253 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.4164 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3281 Z= 0.136 Angle : 0.488 4.415 4462 Z= 0.271 Chirality : 0.035 0.122 531 Planarity : 0.005 0.043 545 Dihedral : 4.261 28.716 486 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.83 % Allowed : 15.85 % Favored : 82.32 % 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: 2.27 (0.40), residues: 416 helix: 1.84 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -1.06 (0.89), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 455 TYR 0.010 0.001 TYR A 116 PHE 0.008 0.001 PHE A 151 TRP 0.020 0.002 TRP A 178 HIS 0.002 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3281) covalent geometry : angle 0.48775 ( 4462) hydrogen bonds : bond 0.05316 ( 284) hydrogen bonds : angle 4.28021 ( 852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 306 MET cc_start: 0.7098 (mtt) cc_final: 0.5955 (tmm) REVERT: A 391 LYS cc_start: 0.7195 (mtpt) cc_final: 0.6980 (mttm) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.6498 time to fit residues: 36.7769 Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.220690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.211209 restraints weight = 10945.801| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 1.29 r_work: 0.4245 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.4157 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3281 Z= 0.151 Angle : 0.502 4.456 4462 Z= 0.280 Chirality : 0.036 0.124 531 Planarity : 0.005 0.045 545 Dihedral : 4.315 27.238 486 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.91 % Allowed : 17.07 % Favored : 82.01 % 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: 2.29 (0.40), residues: 416 helix: 1.87 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -1.18 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.010 0.001 TYR A 116 PHE 0.008 0.001 PHE A 151 TRP 0.020 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3281) covalent geometry : angle 0.50180 ( 4462) hydrogen bonds : bond 0.05477 ( 284) hydrogen bonds : angle 4.32668 ( 852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 306 MET cc_start: 0.7097 (mtt) cc_final: 0.5984 (tmm) outliers start: 3 outliers final: 3 residues processed: 52 average time/residue: 0.5959 time to fit residues: 32.5102 Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 27 optimal weight: 0.0470 chunk 39 optimal weight: 0.0980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.219437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.209765 restraints weight = 10952.733| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 1.30 r_work: 0.4244 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.4155 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3281 Z= 0.152 Angle : 0.507 4.439 4462 Z= 0.282 Chirality : 0.036 0.131 531 Planarity : 0.005 0.046 545 Dihedral : 4.307 26.900 486 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.44 % Allowed : 15.24 % Favored : 82.32 % 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: 2.33 (0.40), residues: 416 helix: 1.89 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -1.18 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.011 0.001 TYR A 116 PHE 0.008 0.001 PHE A 151 TRP 0.020 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3281) covalent geometry : angle 0.50653 ( 4462) hydrogen bonds : bond 0.05467 ( 284) hydrogen bonds : angle 4.32857 ( 852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.7420 (OUTLIER) cc_final: 0.7060 (p) REVERT: A 306 MET cc_start: 0.7093 (mtt) cc_final: 0.5973 (tmm) outliers start: 8 outliers final: 3 residues processed: 56 average time/residue: 0.6101 time to fit residues: 35.8350 Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.217958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.208363 restraints weight = 11112.828| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 1.31 r_work: 0.4195 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.4105 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3281 Z= 0.182 Angle : 0.544 4.488 4462 Z= 0.306 Chirality : 0.037 0.131 531 Planarity : 0.005 0.047 545 Dihedral : 4.547 29.532 486 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.52 % Allowed : 16.46 % Favored : 82.01 % 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: 1.98 (0.40), residues: 416 helix: 1.68 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -1.50 (0.86), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 532 TYR 0.012 0.001 TYR A 116 PHE 0.009 0.001 PHE A 430 TRP 0.020 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3281) covalent geometry : angle 0.54364 ( 4462) hydrogen bonds : bond 0.05925 ( 284) hydrogen bonds : angle 4.48616 ( 852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.7482 (OUTLIER) cc_final: 0.7069 (p) REVERT: A 306 MET cc_start: 0.7062 (mtt) cc_final: 0.5857 (tmm) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.6320 time to fit residues: 37.1533 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.0670 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.0670 chunk 32 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.220360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.211005 restraints weight = 11019.358| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 1.29 r_work: 0.4247 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.4159 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3281 Z= 0.140 Angle : 0.507 4.455 4462 Z= 0.281 Chirality : 0.036 0.141 531 Planarity : 0.005 0.046 545 Dihedral : 4.261 25.743 486 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.91 % Allowed : 17.07 % Favored : 82.01 % 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: 2.35 (0.41), residues: 416 helix: 1.93 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -1.48 (0.83), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 455 TYR 0.009 0.001 TYR A 116 PHE 0.008 0.001 PHE A 151 TRP 0.020 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3281) covalent geometry : angle 0.50728 ( 4462) hydrogen bonds : bond 0.05305 ( 284) hydrogen bonds : angle 4.28982 ( 852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.6982 (mtt) cc_final: 0.5848 (tmm) outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.6493 time to fit residues: 33.9191 Evaluate side-chains 48 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 6 optimal weight: 0.3980 chunk 33 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 9 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 overall best weight: 0.2718 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.221029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.211737 restraints weight = 10959.510| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 1.27 r_work: 0.4265 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.4178 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3281 Z= 0.135 Angle : 0.500 4.447 4462 Z= 0.277 Chirality : 0.036 0.149 531 Planarity : 0.005 0.047 545 Dihedral : 4.175 25.343 486 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.52 % Allowed : 17.38 % Favored : 81.10 % 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: 2.40 (0.40), residues: 416 helix: 1.96 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -1.35 (0.84), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 455 TYR 0.009 0.001 TYR A 116 PHE 0.008 0.001 PHE A 151 TRP 0.021 0.002 TRP A 178 HIS 0.002 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3281) covalent geometry : angle 0.50038 ( 4462) hydrogen bonds : bond 0.05170 ( 284) hydrogen bonds : angle 4.25517 ( 852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.46 seconds wall clock time: 39 minutes 43.69 seconds (2383.69 seconds total)