Starting phenix.real_space_refine on Tue Mar 3 10:53:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xiz_33213/03_2026/7xiz_33213.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xiz_33213/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xiz_33213/03_2026/7xiz_33213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xiz_33213/03_2026/7xiz_33213.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xiz_33213/03_2026/7xiz_33213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xiz_33213/03_2026/7xiz_33213.map" } 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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.71, per 1000 atoms: 0.33 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: 0.17 Conformation dependent library (CDL) restraints added in 98.3 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: 0.06 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: 0.26 Time building geometry restraints manager: 0.25 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 - 21.85: 1170 21.85 - 43.69: 142 43.69 - 65.53: 17 65.53 - 87.37: 8 87.37 - 109.21: 4 Dihedral angle restraints: 1341 sinusoidal: 560 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 1338 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: 0.010 Normalize map: mean=0, sd=1: 2.030 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.330 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 19.025 109.212 832 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 covalent geometry : bond 0.01271 ( 2219) covalent geometry : angle 1.11134 ( 3018) SS BOND : bond 0.00318 ( 3) SS BOND : angle 1.08932 ( 6) hydrogen bonds : bond 0.33402 ( 34) hydrogen bonds : angle 11.41332 ( 87) link_NAG-ASN : bond 0.00847 ( 2) link_NAG-ASN : angle 2.17568 ( 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 : 0.080 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0469 time to fit residues: 1.2839 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 : 0.079 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.077743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.067143 restraints weight = 10080.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.068533 restraints weight = 5871.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069397 restraints weight = 3991.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.070065 restraints weight = 3050.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.070497 restraints weight = 2480.093| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2224 Z= 0.161 Angle : 0.715 6.501 3030 Z= 0.367 Chirality : 0.050 0.150 331 Planarity : 0.007 0.057 393 Dihedral : 13.048 96.006 337 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.09 % Favored : 84.15 % Rotamer: Outliers : 2.98 % Allowed : 37.02 % 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: -3.56 (0.46), residues: 265 helix: -4.40 (0.46), residues: 25 sheet: -1.24 (0.72), residues: 44 loop : -2.55 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.007 0.001 TYR B 473 PHE 0.011 0.001 PHE B 456 TRP 0.006 0.002 TRP B 436 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 2219) covalent geometry : angle 0.71073 ( 3018) SS BOND : bond 0.00356 ( 3) SS BOND : angle 0.80519 ( 6) hydrogen bonds : bond 0.04575 ( 34) hydrogen bonds : angle 7.93509 ( 87) link_NAG-ASN : bond 0.00410 ( 2) link_NAG-ASN : angle 1.91807 ( 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 : 0.079 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 26 average time/residue: 0.0289 time to fit residues: 1.0928 Evaluate side-chains 22 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 538 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.077123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066452 restraints weight = 10140.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.067780 restraints weight = 5954.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.068748 restraints weight = 4098.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.069319 restraints weight = 3121.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069791 restraints weight = 2590.916| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2224 Z= 0.144 Angle : 0.685 5.769 3030 Z= 0.347 Chirality : 0.048 0.157 331 Planarity : 0.006 0.055 393 Dihedral : 12.431 93.058 337 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.47 % Favored : 83.77 % Rotamer: Outliers : 4.68 % Allowed : 34.89 % 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: -3.34 (0.47), residues: 265 helix: -4.26 (0.69), residues: 25 sheet: -0.79 (0.71), residues: 48 loop : -2.51 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 577 TYR 0.006 0.001 TYR B 501 PHE 0.010 0.001 PHE B 456 TRP 0.006 0.002 TRP B 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2219) covalent geometry : angle 0.67933 ( 3018) SS BOND : bond 0.00260 ( 3) SS BOND : angle 0.75787 ( 6) hydrogen bonds : bond 0.04340 ( 34) hydrogen bonds : angle 7.41226 ( 87) link_NAG-ASN : bond 0.00420 ( 2) link_NAG-ASN : angle 1.98278 ( 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 29 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 18 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: B 324 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6449 (mm-30) outliers start: 11 outliers final: 7 residues processed: 28 average time/residue: 0.0294 time to fit residues: 1.1888 Evaluate side-chains 23 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 15 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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 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 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.076478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.066015 restraints weight = 9814.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.067311 restraints weight = 5913.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.068290 restraints weight = 4128.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.068881 restraints weight = 3115.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.069372 restraints weight = 2568.567| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2224 Z= 0.147 Angle : 0.685 7.673 3030 Z= 0.344 Chirality : 0.049 0.161 331 Planarity : 0.006 0.055 393 Dihedral : 12.506 93.499 337 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.47 % Favored : 83.77 % Rotamer: Outliers : 6.81 % Allowed : 33.19 % 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: -3.42 (0.48), residues: 265 helix: -4.49 (0.61), residues: 25 sheet: -1.10 (0.82), residues: 42 loop : -2.42 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 328 TYR 0.008 0.001 TYR B 501 PHE 0.009 0.001 PHE B 456 TRP 0.004 0.002 TRP B 436 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2219) covalent geometry : angle 0.68015 ( 3018) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.65463 ( 6) hydrogen bonds : bond 0.03907 ( 34) hydrogen bonds : angle 7.36293 ( 87) link_NAG-ASN : bond 0.00488 ( 2) link_NAG-ASN : angle 1.90380 ( 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 35 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 324 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6522 (mm-30) outliers start: 16 outliers final: 14 residues processed: 34 average time/residue: 0.0381 time to fit residues: 1.6939 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 : 0.080 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.077328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.066674 restraints weight = 9946.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.068005 restraints weight = 5896.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.068922 restraints weight = 4111.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069533 restraints weight = 3162.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.069891 restraints weight = 2661.036| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 2224 Z= 0.124 Angle : 0.701 7.698 3030 Z= 0.353 Chirality : 0.050 0.178 331 Planarity : 0.006 0.056 393 Dihedral : 12.200 90.749 337 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.47 % Favored : 83.77 % Rotamer: Outliers : 6.38 % Allowed : 34.04 % 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: -3.31 (0.47), residues: 265 helix: -4.89 (0.45), residues: 18 sheet: -1.15 (0.80), residues: 41 loop : -2.37 (0.41), residues: 206 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 0.007 0.001 PHE B 456 TRP 0.007 0.002 TRP B 436 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 2219) covalent geometry : angle 0.68000 ( 3018) SS BOND : bond 0.01249 ( 3) SS BOND : angle 3.35093 ( 6) hydrogen bonds : bond 0.03435 ( 34) hydrogen bonds : angle 7.06800 ( 87) link_NAG-ASN : bond 0.00454 ( 2) link_NAG-ASN : angle 2.10896 ( 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 34 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.087 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 33 average time/residue: 0.0419 time to fit residues: 1.8034 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 : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.076189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065368 restraints weight = 9839.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.066681 restraints weight = 5994.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.067551 restraints weight = 4237.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.068297 restraints weight = 3302.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.068669 restraints weight = 2703.186| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 2224 Z= 0.152 Angle : 0.732 9.796 3030 Z= 0.370 Chirality : 0.050 0.165 331 Planarity : 0.006 0.055 393 Dihedral : 12.353 91.288 337 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.23 % Favored : 83.02 % Rotamer: Outliers : 7.23 % Allowed : 30.64 % Favored : 62.13 % 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: -3.29 (0.48), residues: 265 helix: -4.51 (0.62), residues: 25 sheet: -1.08 (0.81), residues: 41 loop : -2.30 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 328 TYR 0.007 0.001 TYR B 501 PHE 0.009 0.001 PHE B 497 TRP 0.004 0.002 TRP B 353 HIS 0.000 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2219) covalent geometry : angle 0.70220 ( 3018) SS BOND : bond 0.01645 ( 3) SS BOND : angle 4.34136 ( 6) hydrogen bonds : bond 0.03533 ( 34) hydrogen bonds : angle 7.22524 ( 87) link_NAG-ASN : bond 0.00424 ( 2) link_NAG-ASN : angle 1.95638 ( 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: 17 poor density : 19 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: B 324 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6635 (mm-30) REVERT: B 347 PHE cc_start: 0.5682 (OUTLIER) cc_final: 0.5369 (m-10) outliers start: 17 outliers final: 12 residues processed: 36 average time/residue: 0.0407 time to fit residues: 1.8895 Evaluate side-chains 31 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 17 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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 407 VAL 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 4 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 30.0000 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.077646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.066790 restraints weight = 9756.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.068192 restraints weight = 5885.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.069035 restraints weight = 4074.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.069758 restraints weight = 3170.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.070133 restraints weight = 2596.661| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 2224 Z= 0.121 Angle : 0.708 8.181 3030 Z= 0.353 Chirality : 0.049 0.166 331 Planarity : 0.005 0.056 393 Dihedral : 12.013 88.485 337 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.72 % Favored : 84.53 % 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: -3.48 (0.47), residues: 265 helix: -4.76 (0.36), residues: 24 sheet: -1.25 (0.77), residues: 43 loop : -2.42 (0.42), residues: 198 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 0.008 0.001 PHE B 497 TRP 0.006 0.001 TRP B 436 HIS 0.000 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 2219) covalent geometry : angle 0.68298 ( 3018) SS BOND : bond 0.01553 ( 3) SS BOND : angle 3.68749 ( 6) hydrogen bonds : bond 0.03110 ( 34) hydrogen bonds : angle 6.99543 ( 87) link_NAG-ASN : bond 0.00419 ( 2) link_NAG-ASN : angle 2.18542 ( 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 : 0.096 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 32 average time/residue: 0.0421 time to fit residues: 1.7734 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 : 0.081 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.077924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067196 restraints weight = 9946.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.068550 restraints weight = 5929.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.069472 restraints weight = 4141.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.070187 restraints weight = 3217.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.070598 restraints weight = 2637.432| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 2224 Z= 0.119 Angle : 0.705 8.011 3030 Z= 0.351 Chirality : 0.049 0.168 331 Planarity : 0.005 0.057 393 Dihedral : 11.757 85.811 337 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.09 % Favored : 84.15 % Rotamer: Outliers : 4.68 % Allowed : 31.49 % 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: -3.38 (0.48), residues: 265 helix: -4.83 (0.34), residues: 24 sheet: -1.16 (0.78), residues: 43 loop : -2.34 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.006 0.001 TYR B 421 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 covalent geometry : bond 0.00269 ( 2219) covalent geometry : angle 0.68358 ( 3018) SS BOND : bond 0.01373 ( 3) SS BOND : angle 3.27677 ( 6) hydrogen bonds : bond 0.03054 ( 34) hydrogen bonds : angle 6.84494 ( 87) link_NAG-ASN : bond 0.00397 ( 2) link_NAG-ASN : angle 2.20854 ( 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 31 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.078 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 31 average time/residue: 0.0310 time to fit residues: 1.3457 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 : 0.094 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 24 optimal weight: 0.0470 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.076830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.065781 restraints weight = 9998.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.067167 restraints weight = 6104.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.068112 restraints weight = 4281.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.068768 restraints weight = 3327.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.069158 restraints weight = 2766.673| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 2224 Z= 0.145 Angle : 0.750 8.814 3030 Z= 0.371 Chirality : 0.051 0.163 331 Planarity : 0.006 0.055 393 Dihedral : 11.928 85.922 337 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.09 % Favored : 84.15 % Rotamer: Outliers : 5.53 % Allowed : 31.06 % 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: -3.41 (0.48), residues: 265 helix: -4.44 (0.56), residues: 31 sheet: -1.12 (0.81), residues: 41 loop : -2.31 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.005 0.001 TYR B 501 PHE 0.008 0.001 PHE B 497 TRP 0.005 0.002 TRP B 353 HIS 0.000 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 2219) covalent geometry : angle 0.73282 ( 3018) SS BOND : bond 0.01360 ( 3) SS BOND : angle 3.00902 ( 6) hydrogen bonds : bond 0.03244 ( 34) hydrogen bonds : angle 7.02720 ( 87) link_NAG-ASN : bond 0.00354 ( 2) link_NAG-ASN : angle 2.13207 ( 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 30 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 17 time to evaluate : 0.065 Fit side-chains REVERT: B 347 PHE cc_start: 0.5666 (OUTLIER) cc_final: 0.5327 (m-10) outliers start: 13 outliers final: 11 residues processed: 30 average time/residue: 0.0215 time to fit residues: 0.9514 Evaluate side-chains 29 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 0.0060 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.076703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.065783 restraints weight = 9953.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.067189 restraints weight = 6062.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.068168 restraints weight = 4250.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.068745 restraints weight = 3248.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.069224 restraints weight = 2709.808| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3587 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= 0.146 Angle : 0.761 8.463 3030 Z= 0.376 Chirality : 0.051 0.162 331 Planarity : 0.006 0.055 393 Dihedral : 11.940 85.575 337 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.47 % Favored : 83.77 % Rotamer: Outliers : 5.53 % Allowed : 31.49 % Favored : 62.98 % 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: -3.43 (0.48), residues: 265 helix: -4.49 (0.56), residues: 31 sheet: -1.14 (0.81), residues: 41 loop : -2.32 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.009 0.001 TYR B 365 PHE 0.008 0.001 PHE B 497 TRP 0.004 0.002 TRP B 353 HIS 0.000 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 2219) covalent geometry : angle 0.74360 ( 3018) SS BOND : bond 0.01351 ( 3) SS BOND : angle 3.04042 ( 6) hydrogen bonds : bond 0.03292 ( 34) hydrogen bonds : angle 7.01107 ( 87) link_NAG-ASN : bond 0.00387 ( 2) link_NAG-ASN : angle 2.17077 ( 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 31 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 18 time to evaluate : 0.050 Fit side-chains REVERT: B 347 PHE cc_start: 0.5624 (OUTLIER) cc_final: 0.5299 (m-10) REVERT: B 365 TYR cc_start: 0.7455 (m-80) cc_final: 0.7109 (m-80) outliers start: 13 outliers final: 11 residues processed: 31 average time/residue: 0.0207 time to fit residues: 0.9373 Evaluate side-chains 29 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.076323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065347 restraints weight = 10227.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066712 restraints weight = 6208.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.067642 restraints weight = 4375.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.068293 restraints weight = 3380.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.068713 restraints weight = 2831.655| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3703 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= 0.148 Angle : 0.759 8.010 3030 Z= 0.376 Chirality : 0.051 0.158 331 Planarity : 0.006 0.055 393 Dihedral : 11.935 85.081 337 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.47 % Favored : 83.77 % Rotamer: Outliers : 5.53 % Allowed : 31.49 % Favored : 62.98 % 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: -3.44 (0.48), residues: 265 helix: -4.54 (0.53), residues: 31 sheet: -1.13 (0.81), residues: 41 loop : -2.32 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.009 0.001 TYR B 365 PHE 0.007 0.001 PHE B 456 TRP 0.004 0.001 TRP B 353 HIS 0.000 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2219) covalent geometry : angle 0.74226 ( 3018) SS BOND : bond 0.01355 ( 3) SS BOND : angle 2.97280 ( 6) hydrogen bonds : bond 0.03335 ( 34) hydrogen bonds : angle 7.08432 ( 87) link_NAG-ASN : bond 0.00353 ( 2) link_NAG-ASN : angle 2.19948 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 629.02 seconds wall clock time: 11 minutes 25.08 seconds (685.08 seconds total)