Starting phenix.real_space_refine on Wed Jul 1 21:03:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xiz_33213/07_2026/7xiz_33213.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xiz_33213/07_2026/7xiz_33213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xiz_33213/07_2026/7xiz_33213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xiz_33213/07_2026/7xiz_33213.map" model { file = "/net/cci-nas-00/data/ceres_data/7xiz_33213/07_2026/7xiz_33213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xiz_33213/07_2026/7xiz_33213.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xiz_33213/07_2026/7xiz_33213.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xiz_33213/07_2026/7xiz_33213.cif" } resolution = 3.74 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= 0.003 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: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 1386 2.51 5 N 364 2.21 5 O 402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2161 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2133 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.54, per 1000 atoms: 0.25 Number of scatterers: 2161 At special positions: 0 Unit cell: (76.96, 69.68, 76.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 402 8.00 N 364 7.00 C 1386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 Links applied NAG-ASN " NAG B 601 " - " ASN B 331 " " NAG B 602 " - " ASN B 343 " Time building additional restraints: 0.14 Conformation dependent library (CDL) restraints added in 62.0 milliseconds 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 500 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 3 sheets defined 4.5% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.842A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.358A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 538 through 539 removed outlier: 4.825A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 542 through 543 34 hydrogen bonds defined for protein. 87 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: 0.15 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 1 1.13 - 1.30: 345 1.30 - 1.48: 946 1.48 - 1.65: 918 1.65 - 1.82: 9 Bond restraints: 2219 Sorted by residual: bond pdb=" CG PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.503 0.960 0.543 3.40e-02 8.65e+02 2.56e+02 bond pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.473 1.574 -0.101 1.40e-02 5.10e+03 5.22e+01 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" N PRO B 384 " pdb=" CA PRO B 384 " ideal model delta sigma weight residual 1.472 1.439 0.032 1.34e-02 5.57e+03 5.79e+00 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.65e+00 ... (remaining 2214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 3002 4.93 - 9.86: 12 9.86 - 14.79: 1 14.79 - 19.72: 2 19.72 - 24.65: 1 Bond angle restraints: 3018 Sorted by residual: angle pdb=" N PRO B 384 " pdb=" CD PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 103.20 78.55 24.65 1.50e+00 4.44e-01 2.70e+02 angle pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 112.00 96.26 15.74 1.40e+00 5.10e-01 1.26e+02 angle pdb=" CA PRO B 384 " pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 104.50 87.29 17.21 1.90e+00 2.77e-01 8.20e+01 angle pdb=" N PRO B 384 " pdb=" CA PRO B 384 " pdb=" CB PRO B 384 " ideal model delta sigma weight residual 103.26 97.25 6.01 1.14e+00 7.69e-01 2.78e+01 angle pdb=" C PHE B 377 " pdb=" N LYS B 378 " pdb=" CA LYS B 378 " ideal model delta sigma weight residual 121.54 129.63 -8.09 1.91e+00 2.74e-01 1.79e+01 ... (remaining 3013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 1096 18.02 - 36.03: 159 36.03 - 54.04: 37 54.04 - 72.05: 3 72.05 - 90.06: 4 Dihedral angle restraints: 1299 sinusoidal: 518 harmonic: 781 Sorted by residual: dihedral pdb=" CA PHE B 377 " pdb=" C PHE B 377 " pdb=" N LYS B 378 " pdb=" CA LYS B 378 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ILE B 402 " pdb=" C ILE B 402 " pdb=" N ARG B 403 " pdb=" CA ARG B 403 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY B 476 " pdb=" C GLY B 476 " pdb=" N ASN B 477 " pdb=" CA ASN B 477 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 1296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 191 0.039 - 0.078: 83 0.078 - 0.117: 42 0.117 - 0.155: 7 0.155 - 0.194: 8 Chirality restraints: 331 Sorted by residual: chirality pdb=" CB VAL B 367 " pdb=" CA VAL B 367 " pdb=" CG1 VAL B 367 " pdb=" CG2 VAL B 367 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA PHE B 377 " pdb=" N PHE B 377 " pdb=" C PHE B 377 " pdb=" CB PHE B 377 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 328 not shown) Planarity restraints: 395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.097 5.00e-02 4.00e+02 1.34e-01 2.85e+01 pdb=" N PRO B 384 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 378 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C LYS B 378 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS B 378 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS B 379 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO B 521 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.037 5.00e-02 4.00e+02 ... (remaining 392 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 870 2.89 - 3.39: 1887 3.39 - 3.89: 3534 3.89 - 4.40: 3861 4.40 - 4.90: 6428 Nonbonded interactions: 16580 Sorted by model distance: nonbonded pdb=" N ASP B 571 " pdb=" OD1 ASP B 571 " model vdw 2.386 3.120 nonbonded pdb=" O GLN B 563 " pdb=" NH1 ARG B 577 " model vdw 2.395 3.120 nonbonded pdb=" NE2 GLN B 474 " pdb=" O ASN B 477 " model vdw 2.409 3.120 nonbonded pdb=" NE ARG B 457 " pdb=" O SER B 459 " model vdw 2.426 3.120 nonbonded pdb=" OG1 THR B 415 " pdb=" OD2 ASP B 420 " model vdw 2.440 3.040 ... (remaining 16575 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 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: 1.710 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: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.880 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: 0.000 Load rotamer database and sin/cos tables:0.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.013 0.543 2224 Z= 0.438 Angle : 1.114 24.653 3030 Z= 0.634 Chirality : 0.058 0.194 331 Planarity : 0.010 0.134 393 Dihedral : 17.483 90.062 790 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.75 % Allowed : 12.83 % Favored : 86.42 % Rotamer: Outliers : 0.00 % Allowed : 35.32 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.47), residues: 265 helix: -4.15 (0.66), residues: 19 sheet: -1.02 (0.70), residues: 48 loop : -2.57 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 328 TYR 0.007 0.001 TYR B 451 PHE 0.019 0.002 PHE B 377 TRP 0.006 0.001 TRP B 436 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.01271 / 0.44 ( 2219) covalent geometry : angle 1.11134 / 0.63 ( 3018) SS BOND : bond 0.00318 / 0.15 ( 3) SS BOND : angle 1.08932 / 0.59 ( 6) hydrogen bonds : bond 0.33402 / 23.32 ( 34) hydrogen bonds : angle 11.41332 / 8.21 ( 87) link_NAG-ASN : bond 0.00847 / 0.44 ( 2) link_NAG-ASN : angle 2.17568 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0276 time to fit residues: 0.7661 Evaluate side-chains 15 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.077517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.066932 restraints weight = 10086.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.068252 restraints weight = 5893.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.069168 restraints weight = 4040.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.069828 restraints weight = 3054.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.070230 restraints weight = 2516.287| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2224 Z= 0.163 Angle : 0.706 6.734 3030 Z= 0.365 Chirality : 0.050 0.223 331 Planarity : 0.007 0.059 393 Dihedral : 6.111 26.839 295 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.09 % Favored : 84.15 % Rotamer: Outliers : 2.98 % Allowed : 36.60 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.46), residues: 265 helix: -4.44 (0.44), residues: 25 sheet: -1.23 (0.72), residues: 44 loop : -2.54 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 577 TYR 0.007 0.001 TYR B 508 PHE 0.010 0.002 PHE B 456 TRP 0.006 0.002 TRP B 436 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 2219) covalent geometry : angle 0.70632 / 0.37 ( 3018) SS BOND : bond 0.00333 / 0.16 ( 3) SS BOND : angle 0.79468 / 0.41 ( 6) hydrogen bonds : bond 0.04804 / 3.15 ( 34) hydrogen bonds : angle 7.92096 / 5.86 ( 87) link_NAG-ASN : bond 0.00623 / 0.32 ( 2) link_NAG-ASN : angle 0.54037 / 0.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.047 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 26 average time/residue: 0.0180 time to fit residues: 0.6795 Evaluate side-chains 21 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 0.0370 overall best weight: 1.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.078417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.068097 restraints weight = 10049.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.069527 restraints weight = 5784.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.070355 restraints weight = 3891.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.071040 restraints weight = 2961.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.071467 restraints weight = 2390.673| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2224 Z= 0.114 Angle : 0.640 5.726 3030 Z= 0.329 Chirality : 0.047 0.213 331 Planarity : 0.006 0.056 393 Dihedral : 5.608 23.805 295 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.96 % Favored : 85.28 % Rotamer: Outliers : 3.40 % Allowed : 36.60 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.47), residues: 265 helix: -4.66 (0.58), residues: 18 sheet: -0.90 (0.76), residues: 42 loop : -2.37 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 577 TYR 0.007 0.001 TYR B 421 PHE 0.009 0.001 PHE B 456 TRP 0.009 0.002 TRP B 436 HIS 0.000 0.000 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 2219) covalent geometry : angle 0.63907 / 0.33 ( 3018) SS BOND : bond 0.00274 / 0.13 ( 3) SS BOND : angle 0.71845 / 0.38 ( 6) hydrogen bonds : bond 0.03946 / 2.58 ( 34) hydrogen bonds : angle 7.09496 / 5.20 ( 87) link_NAG-ASN : bond 0.00521 / 0.27 ( 2) link_NAG-ASN : angle 1.04284 / 0.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.052 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 26 average time/residue: 0.0208 time to fit residues: 0.7785 Evaluate side-chains 21 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 538 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.075791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.065319 restraints weight = 10053.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066595 restraints weight = 6088.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.067555 restraints weight = 4252.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.068199 restraints weight = 3232.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.068558 restraints weight = 2660.596| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2224 Z= 0.174 Angle : 0.694 7.953 3030 Z= 0.356 Chirality : 0.050 0.205 331 Planarity : 0.007 0.056 393 Dihedral : 6.187 23.967 295 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.23 % Favored : 83.02 % Rotamer: Outliers : 7.23 % Allowed : 33.19 % Favored : 59.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.47), residues: 265 helix: -4.58 (0.51), residues: 26 sheet: -1.07 (0.78), residues: 43 loop : -2.39 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 328 TYR 0.009 0.001 TYR B 501 PHE 0.011 0.001 PHE B 456 TRP 0.007 0.002 TRP B 353 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 2219) covalent geometry : angle 0.69416 / 0.36 ( 3018) SS BOND : bond 0.00253 / 0.13 ( 3) SS BOND : angle 0.81935 / 0.38 ( 6) hydrogen bonds : bond 0.04257 / 2.67 ( 34) hydrogen bonds : angle 7.42727 / 5.44 ( 87) link_NAG-ASN : bond 0.00616 / 0.32 ( 2) link_NAG-ASN : angle 0.50630 / 0.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 19 time to evaluate : 0.053 Fit side-chains revert: symmetry clash REVERT: B 324 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6474 (mm-30) REVERT: B 347 PHE cc_start: 0.5686 (OUTLIER) cc_final: 0.5393 (m-10) outliers start: 17 outliers final: 14 residues processed: 35 average time/residue: 0.0263 time to fit residues: 1.1956 Evaluate side-chains 33 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 17 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 0.0570 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.077245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.066705 restraints weight = 9755.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.068048 restraints weight = 5804.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.069035 restraints weight = 4027.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.069652 restraints weight = 3044.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.069994 restraints weight = 2484.272| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 2224 Z= 0.122 Angle : 0.675 7.129 3030 Z= 0.346 Chirality : 0.049 0.206 331 Planarity : 0.006 0.056 393 Dihedral : 5.751 26.130 295 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.34 % Favored : 84.91 % Rotamer: Outliers : 6.81 % Allowed : 32.34 % Favored : 60.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.46), residues: 265 helix: -4.93 (0.44), residues: 18 sheet: -1.16 (0.84), residues: 33 loop : -2.37 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 577 TYR 0.008 0.001 TYR B 421 PHE 0.007 0.001 PHE B 456 TRP 0.008 0.002 TRP B 436 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 2219) covalent geometry : angle 0.66002 / 0.34 ( 3018) SS BOND : bond 0.01331 / 0.63 ( 3) SS BOND : angle 3.15612 / 1.65 ( 6) hydrogen bonds : bond 0.03341 / 2.19 ( 34) hydrogen bonds : angle 6.97125 / 5.11 ( 87) link_NAG-ASN : bond 0.00580 / 0.30 ( 2) link_NAG-ASN : angle 1.15269 / 0.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 0.049 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 34 average time/residue: 0.0252 time to fit residues: 1.1237 Evaluate side-chains 28 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 17 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 0.0770 chunk 6 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.078529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.067840 restraints weight = 9588.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069173 restraints weight = 5802.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.070185 restraints weight = 4082.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.070744 restraints weight = 3106.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.071095 restraints weight = 2576.942| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 2224 Z= 0.115 Angle : 0.673 9.019 3030 Z= 0.344 Chirality : 0.049 0.219 331 Planarity : 0.005 0.056 393 Dihedral : 5.484 18.947 295 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.09 % Favored : 84.15 % Rotamer: Outliers : 5.96 % Allowed : 29.79 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.48), residues: 265 helix: -4.96 (0.43), residues: 18 sheet: -1.07 (0.77), residues: 43 loop : -2.27 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 577 TYR 0.008 0.001 TYR B 421 PHE 0.007 0.001 PHE B 429 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 2219) covalent geometry : angle 0.64735 / 0.33 ( 3018) SS BOND : bond 0.01344 / 0.64 ( 3) SS BOND : angle 4.06697 / 2.16 ( 6) hydrogen bonds : bond 0.02975 / 1.99 ( 34) hydrogen bonds : angle 6.63792 / 4.88 ( 87) link_NAG-ASN : bond 0.00542 / 0.28 ( 2) link_NAG-ASN : angle 1.03254 / 0.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 22 time to evaluate : 0.085 Fit side-chains REVERT: B 347 PHE cc_start: 0.5351 (OUTLIER) cc_final: 0.5094 (m-10) outliers start: 14 outliers final: 9 residues processed: 34 average time/residue: 0.0366 time to fit residues: 1.6742 Evaluate side-chains 28 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 18 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.075353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.064657 restraints weight = 10086.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.065924 restraints weight = 6128.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.066850 restraints weight = 4334.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.067526 restraints weight = 3361.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.067900 restraints weight = 2772.201| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 2224 Z= 0.186 Angle : 0.751 7.944 3030 Z= 0.383 Chirality : 0.052 0.199 331 Planarity : 0.006 0.054 393 Dihedral : 6.175 23.270 295 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.60 % Favored : 82.64 % Rotamer: Outliers : 5.96 % Allowed : 30.21 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.49), residues: 265 helix: -4.43 (0.61), residues: 25 sheet: -0.83 (0.75), residues: 47 loop : -2.32 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.008 0.001 TYR B 396 PHE 0.010 0.002 PHE B 497 TRP 0.007 0.002 TRP B 353 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 2219) covalent geometry : angle 0.73614 / 0.38 ( 3018) SS BOND : bond 0.01649 / 0.79 ( 3) SS BOND : angle 3.49706 / 1.81 ( 6) hydrogen bonds : bond 0.03711 / 2.34 ( 34) hydrogen bonds : angle 7.36190 / 5.45 ( 87) link_NAG-ASN : bond 0.00551 / 0.29 ( 2) link_NAG-ASN : angle 0.59445 / 0.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 0.103 Fit side-chains REVERT: B 347 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.5233 (m-10) outliers start: 14 outliers final: 10 residues processed: 32 average time/residue: 0.0272 time to fit residues: 1.2753 Evaluate side-chains 27 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 16 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.075733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.064922 restraints weight = 10088.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066299 restraints weight = 6116.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.067197 restraints weight = 4280.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.067860 restraints weight = 3331.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.068140 restraints weight = 2749.101| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 2224 Z= 0.163 Angle : 0.753 8.794 3030 Z= 0.377 Chirality : 0.051 0.201 331 Planarity : 0.006 0.054 393 Dihedral : 6.138 22.274 295 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.23 % Favored : 83.02 % Rotamer: Outliers : 6.38 % Allowed : 30.21 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.48), residues: 265 helix: -4.45 (0.53), residues: 31 sheet: -1.15 (0.81), residues: 41 loop : -2.46 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 328 TYR 0.015 0.001 TYR B 365 PHE 0.009 0.001 PHE B 497 TRP 0.004 0.002 TRP B 353 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 2219) covalent geometry : angle 0.73937 / 0.37 ( 3018) SS BOND : bond 0.01468 / 0.70 ( 3) SS BOND : angle 3.23890 / 1.69 ( 6) hydrogen bonds : bond 0.03446 / 2.20 ( 34) hydrogen bonds : angle 7.29500 / 5.46 ( 87) link_NAG-ASN : bond 0.00576 / 0.30 ( 2) link_NAG-ASN : angle 0.83771 / 0.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.081 Fit side-chains REVERT: B 347 PHE cc_start: 0.5689 (OUTLIER) cc_final: 0.5207 (m-10) outliers start: 15 outliers final: 14 residues processed: 33 average time/residue: 0.0268 time to fit residues: 1.2839 Evaluate side-chains 32 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 17 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.075771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.064885 restraints weight = 9982.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066210 restraints weight = 6101.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.067114 restraints weight = 4320.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.067818 restraints weight = 3363.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.068237 restraints weight = 2773.597| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2224 Z= 0.159 Angle : 0.762 8.541 3030 Z= 0.383 Chirality : 0.052 0.201 331 Planarity : 0.006 0.055 393 Dihedral : 6.133 22.341 295 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.60 % Favored : 82.64 % Rotamer: Outliers : 6.38 % Allowed : 31.06 % Favored : 62.55 % 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 are not related in a simple way. whole: -3.58 (0.48), residues: 265 helix: -4.56 (0.53), residues: 31 sheet: -1.17 (0.81), residues: 41 loop : -2.46 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 328 TYR 0.015 0.001 TYR B 365 PHE 0.009 0.001 PHE B 497 TRP 0.004 0.002 TRP B 353 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 2219) covalent geometry : angle 0.74938 / 0.38 ( 3018) SS BOND : bond 0.01446 / 0.69 ( 3) SS BOND : angle 3.15559 / 1.65 ( 6) hydrogen bonds : bond 0.03621 / 2.27 ( 34) hydrogen bonds : angle 7.27941 / 5.49 ( 87) link_NAG-ASN : bond 0.00570 / 0.30 ( 2) link_NAG-ASN : angle 0.85703 / 0.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 18 time to evaluate : 0.097 Fit side-chains REVERT: B 347 PHE cc_start: 0.5687 (OUTLIER) cc_final: 0.5177 (m-10) outliers start: 15 outliers final: 14 residues processed: 33 average time/residue: 0.0250 time to fit residues: 1.1847 Evaluate side-chains 32 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 17 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.0670 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.077298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066259 restraints weight = 9888.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.067700 restraints weight = 6069.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.068690 restraints weight = 4256.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069208 restraints weight = 3260.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.069757 restraints weight = 2754.039| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 2224 Z= 0.125 Angle : 0.742 9.878 3030 Z= 0.369 Chirality : 0.050 0.208 331 Planarity : 0.005 0.056 393 Dihedral : 5.828 21.252 295 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.72 % Favored : 84.53 % Rotamer: Outliers : 5.53 % Allowed : 31.91 % Favored : 62.55 % 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 are not related in a simple way. whole: -3.54 (0.47), residues: 265 helix: -4.96 (0.33), residues: 24 sheet: -1.29 (0.78), residues: 43 loop : -2.44 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.013 0.001 TYR B 365 PHE 0.008 0.001 PHE B 497 TRP 0.006 0.001 TRP B 436 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 2219) covalent geometry : angle 0.72947 / 0.36 ( 3018) SS BOND : bond 0.01333 / 0.63 ( 3) SS BOND : angle 3.02450 / 1.60 ( 6) hydrogen bonds : bond 0.03167 / 2.10 ( 34) hydrogen bonds : angle 6.90319 / 5.22 ( 87) link_NAG-ASN : bond 0.00592 / 0.31 ( 2) link_NAG-ASN : angle 1.14590 / 0.67 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 17 time to evaluate : 0.095 Fit side-chains REVERT: B 347 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.5381 (m-10) outliers start: 13 outliers final: 11 residues processed: 28 average time/residue: 0.0291 time to fit residues: 1.2021 Evaluate side-chains 28 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 16 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 0.0030 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.076669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065611 restraints weight = 10122.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.066982 restraints weight = 6197.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.067995 restraints weight = 4384.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.068585 restraints weight = 3366.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.069139 restraints weight = 2809.612| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 2224 Z= 0.137 Angle : 0.732 8.350 3030 Z= 0.368 Chirality : 0.051 0.207 331 Planarity : 0.006 0.056 393 Dihedral : 5.874 21.675 295 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.23 % Favored : 83.02 % Rotamer: Outliers : 5.96 % Allowed : 30.64 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.48), residues: 265 helix: -4.51 (0.58), residues: 31 sheet: -1.25 (0.78), residues: 43 loop : -2.39 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.011 0.001 TYR B 365 PHE 0.008 0.001 PHE B 497 TRP 0.004 0.001 TRP B 353 HIS 0.000 0.000 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 2219) covalent geometry : angle 0.71964 / 0.36 ( 3018) SS BOND : bond 0.01329 / 0.63 ( 3) SS BOND : angle 3.00315 / 1.58 ( 6) hydrogen bonds : bond 0.03275 / 2.11 ( 34) hydrogen bonds : angle 6.91885 / 5.27 ( 87) link_NAG-ASN : bond 0.00568 / 0.30 ( 2) link_NAG-ASN : angle 0.86818 / 0.52 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 587.99 seconds wall clock time: 10 minutes 46.87 seconds (646.87 seconds total)