Starting phenix.real_space_refine on Wed Jul 1 22:45:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xuu_38684/07_2026/8xuu_38684.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xuu_38684/07_2026/8xuu_38684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xuu_38684/07_2026/8xuu_38684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xuu_38684/07_2026/8xuu_38684.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xuu_38684/07_2026/8xuu_38684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xuu_38684/07_2026/8xuu_38684.map" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.057 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 15 5.16 5 C 2322 2.51 5 N 577 2.21 5 O 684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 3598 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3474 Classifications: {'peptide': 431} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 406} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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 Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 99 Unusual residues: {'IDU': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 0.79, per 1000 atoms: 0.22 Number of scatterers: 3598 At special positions: 0 Unit cell: (73.84, 85.28, 88.4, 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 15 16.00 O 684 8.00 N 577 7.00 C 2322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 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 BETA1-4 " NAG B 1 " - " BMA B 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 331 " " NAG A1307 " - " ASN A 61 " " NAG B 1 " - " ASN A 282 " Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 123.1 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 810 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 8.8% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.813A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.850A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.580A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 removed outlier: 3.523A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.873A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.071A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 118 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.704A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.722A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) 79 hydrogen bonds defined for protein. 204 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: 0.50 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 610 1.32 - 1.44: 1086 1.44 - 1.57: 1987 1.57 - 1.69: 1 1.69 - 1.81: 15 Bond restraints: 3699 Sorted by residual: bond pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta sigma weight residual 1.443 1.506 -0.064 1.37e-02 5.33e+03 2.17e+01 bond pdb=" CA PHE A 216 " pdb=" C PHE A 216 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.26e-02 6.30e+03 1.29e+01 bond pdb=" N VAL A 332 " pdb=" CA VAL A 332 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.10e+01 bond pdb=" N SER A 60 " pdb=" CA SER A 60 " ideal model delta sigma weight residual 1.459 1.488 -0.029 9.10e-03 1.21e+04 9.84e+00 bond pdb=" N VAL A 382 " pdb=" CA VAL A 382 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.14e-02 7.69e+03 9.59e+00 ... (remaining 3694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 4582 2.17 - 4.34: 401 4.34 - 6.52: 41 6.52 - 8.69: 4 8.69 - 10.86: 2 Bond angle restraints: 5030 Sorted by residual: angle pdb=" CA VAL A 171 " pdb=" C VAL A 171 " pdb=" O VAL A 171 " ideal model delta sigma weight residual 121.68 117.33 4.35 7.90e-01 1.60e+00 3.03e+01 angle pdb=" N PRO A 373 " pdb=" CA PRO A 373 " pdb=" C PRO A 373 " ideal model delta sigma weight residual 112.47 101.61 10.86 2.06e+00 2.36e-01 2.78e+01 angle pdb=" N PHE A 375 " pdb=" CA PHE A 375 " pdb=" C PHE A 375 " ideal model delta sigma weight residual 113.41 107.18 6.23 1.22e+00 6.72e-01 2.61e+01 angle pdb=" CA ILE A 212 " pdb=" C ILE A 212 " pdb=" O ILE A 212 " ideal model delta sigma weight residual 122.63 118.29 4.34 8.70e-01 1.32e+00 2.49e+01 angle pdb=" N LYS A 481 " pdb=" CA LYS A 481 " pdb=" C LYS A 481 " ideal model delta sigma weight residual 113.23 107.17 6.06 1.22e+00 6.72e-01 2.47e+01 ... (remaining 5025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 2059 22.93 - 45.86: 160 45.86 - 68.79: 36 68.79 - 91.72: 10 91.72 - 114.65: 15 Dihedral angle restraints: 2280 sinusoidal: 1017 harmonic: 1263 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 17.18 75.82 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -49.19 -36.81 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CA THR A 500 " pdb=" C THR A 500 " pdb=" N TYR A 501 " pdb=" CA TYR A 501 " ideal model delta harmonic sigma weight residual 180.00 160.07 19.93 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 2277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 559 0.307 - 0.613: 3 0.613 - 0.920: 0 0.920 - 1.227: 0 1.227 - 1.534: 1 Chirality restraints: 563 Sorted by residual: chirality pdb=" C1 BMA B 2 " pdb=" O4 NAG B 1 " pdb=" C2 BMA B 2 " pdb=" O5 BMA B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.12e+02 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-01 2.50e+01 5.88e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 560 not shown) Planarity restraints: 642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " 0.335 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG A1303 " -0.088 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " 0.178 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.291 2.00e-02 2.50e+03 2.46e-01 7.56e+02 pdb=" C7 NAG A1304 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.423 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.184 2.00e-02 2.50e+03 1.58e-01 3.11e+02 pdb=" C7 NAG A1301 " 0.033 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.029 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.262 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.141 2.00e-02 2.50e+03 ... (remaining 639 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 781 2.78 - 3.31: 3287 3.31 - 3.84: 5760 3.84 - 4.37: 6886 4.37 - 4.90: 11361 Nonbonded interactions: 28075 Sorted by model distance: nonbonded pdb=" ND2 ASN A 422 " pdb=" O ARG A 454 " model vdw 2.253 3.120 nonbonded pdb=" N GLY A 485 " pdb=" O CYS A 488 " model vdw 2.276 3.120 nonbonded pdb=" O HIS A 445 " pdb=" OG SER A 446 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLU A 96 " pdb=" N ILE A 100 " model vdw 2.313 3.120 nonbonded pdb=" NH2 ARG A 34 " pdb=" O PRO A 217 " model vdw 2.318 3.120 ... (remaining 28070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.710 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 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 : 0.009 0.065 3713 Z= 0.628 Angle : 1.264 10.859 5066 Z= 0.824 Chirality : 0.102 1.534 563 Planarity : 0.019 0.285 635 Dihedral : 19.771 114.649 1452 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.25 % Favored : 85.04 % Rotamer: Outliers : 2.09 % Allowed : 18.85 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.45 (0.39), residues: 421 helix: -1.92 (0.95), residues: 30 sheet: -1.78 (0.47), residues: 114 loop : -2.72 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.029 0.002 TYR A 501 PHE 0.020 0.002 PHE A 55 TRP 0.027 0.003 TRP A 452 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00896 / 0.63 ( 3699) covalent geometry : angle 1.23974 / 0.82 ( 5030) SS BOND : bond 0.00522 / 0.31 ( 6) SS BOND : angle 1.08463 / 0.67 ( 12) hydrogen bonds : bond 0.20437 / 13.89 ( 79) hydrogen bonds : angle 10.07884 / 6.36 ( 204) link_BETA1-4 : bond 0.00836 / 0.44 ( 1) link_BETA1-4 : angle 2.57030 / 1.39 ( 3) link_NAG-ASN : bond 0.00607 / 0.31 ( 7) link_NAG-ASN : angle 3.97162 / 2.29 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7032 (ptpt) cc_final: 0.6426 (tttm) REVERT: A 278 LYS cc_start: 0.8836 (tmtt) cc_final: 0.8627 (tttm) REVERT: A 396 TYR cc_start: 0.7739 (m-80) cc_final: 0.7348 (m-80) REVERT: A 508 TYR cc_start: 0.7309 (m-80) cc_final: 0.7022 (m-80) outliers start: 8 outliers final: 1 residues processed: 95 average time/residue: 0.0607 time to fit residues: 7.1014 Evaluate side-chains 42 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.0060 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 125 ASN A 218 GLN A 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.164706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.131887 restraints weight = 5449.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.136325 restraints weight = 3475.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.139493 restraints weight = 2569.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.141711 restraints weight = 2075.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.143263 restraints weight = 1777.547| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3713 Z= 0.149 Angle : 0.806 10.441 5066 Z= 0.372 Chirality : 0.049 0.189 563 Planarity : 0.004 0.031 635 Dihedral : 14.020 94.992 658 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 4.45 % Allowed : 18.06 % Favored : 77.49 % 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: -3.10 (0.39), residues: 421 helix: -1.58 (0.88), residues: 36 sheet: -1.52 (0.48), residues: 117 loop : -2.50 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 466 TYR 0.029 0.002 TYR A 265 PHE 0.015 0.001 PHE A 338 TRP 0.026 0.002 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 3699) covalent geometry : angle 0.75009 / 0.36 ( 5030) SS BOND : bond 0.00525 / 0.23 ( 6) SS BOND : angle 0.88715 / 0.47 ( 12) hydrogen bonds : bond 0.03778 / 2.54 ( 79) hydrogen bonds : angle 7.31242 / 4.68 ( 204) link_BETA1-4 : bond 0.00222 / 0.12 ( 1) link_BETA1-4 : angle 2.46257 / 1.28 ( 3) link_NAG-ASN : bond 0.00408 / 0.18 ( 7) link_NAG-ASN : angle 4.52148 / 2.65 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 278 LYS cc_start: 0.8855 (tmtt) cc_final: 0.8592 (tttm) REVERT: A 298 GLU cc_start: 0.7989 (tt0) cc_final: 0.7767 (tt0) outliers start: 17 outliers final: 11 residues processed: 55 average time/residue: 0.0472 time to fit residues: 3.6049 Evaluate side-chains 43 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 439 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.161822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.128136 restraints weight = 5437.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.132442 restraints weight = 3535.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.135563 restraints weight = 2642.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.137604 restraints weight = 2152.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.139076 restraints weight = 1870.104| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3713 Z= 0.134 Angle : 0.717 8.641 5066 Z= 0.332 Chirality : 0.048 0.224 563 Planarity : 0.004 0.036 635 Dihedral : 12.342 92.261 657 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.98 % Favored : 89.79 % Rotamer: Outliers : 4.45 % Allowed : 18.59 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.98 (0.40), residues: 421 helix: -1.38 (0.87), residues: 37 sheet: -1.54 (0.47), residues: 127 loop : -2.39 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 102 TYR 0.022 0.001 TYR A 265 PHE 0.013 0.001 PHE A 347 TRP 0.021 0.002 TRP A 436 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 3699) covalent geometry : angle 0.67844 / 0.32 ( 5030) SS BOND : bond 0.00331 / 0.15 ( 6) SS BOND : angle 0.57738 / 0.32 ( 12) hydrogen bonds : bond 0.03608 / 2.49 ( 79) hydrogen bonds : angle 6.64099 / 4.27 ( 204) link_BETA1-4 : bond 0.00413 / 0.22 ( 1) link_BETA1-4 : angle 1.46759 / 0.79 ( 3) link_NAG-ASN : bond 0.00397 / 0.18 ( 7) link_NAG-ASN : angle 3.64542 / 2.12 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.084 Fit side-chains REVERT: A 378 LYS cc_start: 0.8028 (tptt) cc_final: 0.7727 (mtmm) REVERT: A 396 TYR cc_start: 0.7696 (m-80) cc_final: 0.7247 (m-10) REVERT: A 438 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 468 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7768 (tt) outliers start: 17 outliers final: 12 residues processed: 53 average time/residue: 0.0462 time to fit residues: 3.2674 Evaluate side-chains 44 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.161881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.129056 restraints weight = 5430.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.131538 restraints weight = 4376.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.133799 restraints weight = 3329.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.134230 restraints weight = 2704.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.137290 restraints weight = 2579.491| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3713 Z= 0.128 Angle : 0.676 8.970 5066 Z= 0.314 Chirality : 0.047 0.212 563 Planarity : 0.004 0.035 635 Dihedral : 10.712 85.116 657 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.98 % Favored : 89.79 % Rotamer: Outliers : 5.50 % Allowed : 18.59 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.74 (0.40), residues: 421 helix: -1.28 (0.88), residues: 37 sheet: -1.21 (0.49), residues: 119 loop : -2.31 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.021 0.001 TYR A 265 PHE 0.013 0.001 PHE A 194 TRP 0.022 0.002 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 3699) covalent geometry : angle 0.64273 / 0.31 ( 5030) SS BOND : bond 0.00351 / 0.14 ( 6) SS BOND : angle 0.52112 / 0.29 ( 12) hydrogen bonds : bond 0.03260 / 2.24 ( 79) hydrogen bonds : angle 6.08135 / 3.96 ( 204) link_BETA1-4 : bond 0.00656 / 0.35 ( 1) link_BETA1-4 : angle 1.43400 / 0.79 ( 3) link_NAG-ASN : bond 0.00415 / 0.21 ( 7) link_NAG-ASN : angle 3.31094 / 1.95 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.116 Fit side-chains REVERT: A 129 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6173 (ptmm) REVERT: A 392 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: A 396 TYR cc_start: 0.7819 (m-80) cc_final: 0.7433 (m-10) REVERT: A 468 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7817 (tt) outliers start: 21 outliers final: 15 residues processed: 56 average time/residue: 0.0407 time to fit residues: 3.0484 Evaluate side-chains 48 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.157850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.125789 restraints weight = 5446.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.129577 restraints weight = 3625.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.132226 restraints weight = 2755.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.134053 restraints weight = 2277.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.135058 restraints weight = 1990.049| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3713 Z= 0.159 Angle : 0.702 8.827 5066 Z= 0.328 Chirality : 0.047 0.192 563 Planarity : 0.005 0.056 635 Dihedral : 9.656 76.270 657 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.88 % Favored : 87.89 % Rotamer: Outliers : 5.24 % Allowed : 20.68 % Favored : 74.08 % 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: -2.71 (0.40), residues: 421 helix: -1.11 (0.88), residues: 36 sheet: -1.22 (0.48), residues: 128 loop : -2.30 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 498 TYR 0.026 0.002 TYR A 265 PHE 0.014 0.002 PHE A 194 TRP 0.020 0.002 TRP A 436 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 3699) covalent geometry : angle 0.67090 / 0.32 ( 5030) SS BOND : bond 0.00160 / 0.08 ( 6) SS BOND : angle 0.46037 / 0.25 ( 12) hydrogen bonds : bond 0.03357 / 2.26 ( 79) hydrogen bonds : angle 6.21385 / 4.01 ( 204) link_BETA1-4 : bond 0.00513 / 0.27 ( 1) link_BETA1-4 : angle 1.57107 / 0.88 ( 3) link_NAG-ASN : bond 0.00404 / 0.20 ( 7) link_NAG-ASN : angle 3.27102 / 1.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 34 time to evaluate : 0.135 Fit side-chains REVERT: A 129 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6254 (ptmm) REVERT: A 354 ASN cc_start: 0.8546 (t0) cc_final: 0.8207 (p0) REVERT: A 392 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: A 396 TYR cc_start: 0.7960 (m-80) cc_final: 0.7624 (m-10) REVERT: A 468 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.7890 (tt) outliers start: 20 outliers final: 16 residues processed: 50 average time/residue: 0.0396 time to fit residues: 2.8029 Evaluate side-chains 47 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 28 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.160895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125097 restraints weight = 5590.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.129321 restraints weight = 3720.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.132374 restraints weight = 2855.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.134411 restraints weight = 2383.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.135640 restraints weight = 2101.975| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3713 Z= 0.119 Angle : 0.661 8.359 5066 Z= 0.303 Chirality : 0.045 0.160 563 Planarity : 0.004 0.046 635 Dihedral : 8.477 68.037 657 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.26 % Favored : 90.50 % Rotamer: Outliers : 5.24 % Allowed : 21.73 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.63 (0.40), residues: 421 helix: -1.03 (0.90), residues: 36 sheet: -1.00 (0.50), residues: 119 loop : -2.32 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.013 0.001 TYR A 265 PHE 0.007 0.001 PHE A 194 TRP 0.014 0.002 TRP A 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 3699) covalent geometry : angle 0.62472 / 0.29 ( 5030) SS BOND : bond 0.00228 / 0.09 ( 6) SS BOND : angle 0.43741 / 0.24 ( 12) hydrogen bonds : bond 0.02837 / 1.92 ( 79) hydrogen bonds : angle 5.94403 / 3.85 ( 204) link_BETA1-4 : bond 0.00495 / 0.26 ( 1) link_BETA1-4 : angle 1.46110 / 0.81 ( 3) link_NAG-ASN : bond 0.00360 / 0.18 ( 7) link_NAG-ASN : angle 3.37452 / 2.05 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 32 time to evaluate : 0.084 Fit side-chains REVERT: A 129 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6246 (ptmm) REVERT: A 354 ASN cc_start: 0.8522 (t0) cc_final: 0.8220 (p0) REVERT: A 392 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8183 (m-80) REVERT: A 396 TYR cc_start: 0.7897 (m-80) cc_final: 0.7526 (m-10) REVERT: A 468 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.7892 (tt) outliers start: 20 outliers final: 16 residues processed: 49 average time/residue: 0.0309 time to fit residues: 2.2649 Evaluate side-chains 47 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 28 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.158881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125169 restraints weight = 5657.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.128445 restraints weight = 3736.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.128871 restraints weight = 3197.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.129854 restraints weight = 2878.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.131216 restraints weight = 2686.014| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3713 Z= 0.142 Angle : 0.670 7.705 5066 Z= 0.311 Chirality : 0.045 0.147 563 Planarity : 0.004 0.043 635 Dihedral : 7.873 60.449 657 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.93 % Favored : 88.84 % Rotamer: Outliers : 5.24 % Allowed : 21.73 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.60 (0.40), residues: 421 helix: -1.09 (0.88), residues: 36 sheet: -1.03 (0.49), residues: 124 loop : -2.27 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.019 0.001 TYR A 265 PHE 0.011 0.001 PHE A 194 TRP 0.016 0.002 TRP A 436 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 3699) covalent geometry : angle 0.63481 / 0.30 ( 5030) SS BOND : bond 0.00282 / 0.12 ( 6) SS BOND : angle 0.43515 / 0.24 ( 12) hydrogen bonds : bond 0.03075 / 2.08 ( 79) hydrogen bonds : angle 5.99080 / 3.90 ( 204) link_BETA1-4 : bond 0.00450 / 0.24 ( 1) link_BETA1-4 : angle 1.48396 / 0.83 ( 3) link_NAG-ASN : bond 0.00367 / 0.18 ( 7) link_NAG-ASN : angle 3.36719 / 2.06 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.101 Fit side-chains REVERT: A 129 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6244 (ptmm) REVERT: A 392 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8156 (m-80) REVERT: A 396 TYR cc_start: 0.7958 (m-80) cc_final: 0.7597 (m-10) REVERT: A 468 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.7946 (tt) outliers start: 20 outliers final: 15 residues processed: 48 average time/residue: 0.0310 time to fit residues: 2.1948 Evaluate side-chains 44 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.159257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.123932 restraints weight = 5659.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.127939 restraints weight = 3852.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.130760 restraints weight = 2988.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.132471 restraints weight = 2517.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.133941 restraints weight = 2240.972| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3713 Z= 0.117 Angle : 0.650 8.483 5066 Z= 0.299 Chirality : 0.044 0.129 563 Planarity : 0.004 0.040 635 Dihedral : 7.000 50.673 657 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.50 % Favored : 90.26 % Rotamer: Outliers : 5.24 % Allowed : 21.99 % Favored : 72.77 % 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: -2.58 (0.40), residues: 421 helix: -1.12 (0.88), residues: 36 sheet: -1.01 (0.50), residues: 124 loop : -2.27 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.014 0.001 TYR A 265 PHE 0.008 0.001 PHE A 194 TRP 0.017 0.002 TRP A 436 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 3699) covalent geometry : angle 0.61115 / 0.29 ( 5030) SS BOND : bond 0.00151 / 0.07 ( 6) SS BOND : angle 0.36837 / 0.20 ( 12) hydrogen bonds : bond 0.02857 / 1.96 ( 79) hydrogen bonds : angle 5.88903 / 3.83 ( 204) link_BETA1-4 : bond 0.00569 / 0.30 ( 1) link_BETA1-4 : angle 1.50153 / 0.83 ( 3) link_NAG-ASN : bond 0.00304 / 0.15 ( 7) link_NAG-ASN : angle 3.45897 / 2.12 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 29 time to evaluate : 0.092 Fit side-chains REVERT: A 129 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6218 (ptmm) REVERT: A 392 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8181 (m-80) REVERT: A 396 TYR cc_start: 0.7934 (m-80) cc_final: 0.7583 (m-10) REVERT: A 468 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.7966 (tt) outliers start: 20 outliers final: 15 residues processed: 46 average time/residue: 0.0340 time to fit residues: 2.1785 Evaluate side-chains 45 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 27 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 6 optimal weight: 0.3980 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.160409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125343 restraints weight = 5630.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.129526 restraints weight = 3785.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.132351 restraints weight = 2919.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.134414 restraints weight = 2444.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.135756 restraints weight = 2155.206| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.6561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3713 Z= 0.097 Angle : 0.618 8.278 5066 Z= 0.284 Chirality : 0.043 0.130 563 Planarity : 0.004 0.040 635 Dihedral : 5.911 41.287 657 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.98 % Favored : 89.79 % Rotamer: Outliers : 4.19 % Allowed : 22.51 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.41), residues: 421 helix: -0.18 (1.21), residues: 23 sheet: -0.98 (0.49), residues: 126 loop : -1.91 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 498 TYR 0.012 0.001 TYR A 170 PHE 0.007 0.001 PHE A 194 TRP 0.014 0.002 TRP A 436 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 3699) covalent geometry : angle 0.58117 / 0.28 ( 5030) SS BOND : bond 0.00160 / 0.07 ( 6) SS BOND : angle 0.36504 / 0.20 ( 12) hydrogen bonds : bond 0.02600 / 1.77 ( 79) hydrogen bonds : angle 5.68560 / 3.69 ( 204) link_BETA1-4 : bond 0.00584 / 0.31 ( 1) link_BETA1-4 : angle 1.45916 / 0.80 ( 3) link_NAG-ASN : bond 0.00225 / 0.11 ( 7) link_NAG-ASN : angle 3.27607 / 2.00 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.191 Fit side-chains REVERT: A 129 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6137 (ptmm) REVERT: A 392 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: A 396 TYR cc_start: 0.7918 (m-80) cc_final: 0.7538 (m-10) REVERT: A 468 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.7968 (tt) REVERT: A 511 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7892 (t) outliers start: 16 outliers final: 12 residues processed: 47 average time/residue: 0.0560 time to fit residues: 3.6795 Evaluate side-chains 43 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 27 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.0770 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.158767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.123665 restraints weight = 5646.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.127750 restraints weight = 3800.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.130603 restraints weight = 2930.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.132405 restraints weight = 2461.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.133846 restraints weight = 2185.575| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.6709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3713 Z= 0.105 Angle : 0.611 8.806 5066 Z= 0.284 Chirality : 0.043 0.129 563 Planarity : 0.004 0.041 635 Dihedral : 5.382 40.413 657 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.50 % Favored : 90.26 % Rotamer: Outliers : 4.71 % Allowed : 23.30 % Favored : 71.99 % 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: -2.33 (0.41), residues: 421 helix: -0.61 (1.00), residues: 29 sheet: -0.97 (0.49), residues: 128 loop : -2.04 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.015 0.001 TYR A 265 PHE 0.008 0.001 PHE A 329 TRP 0.016 0.001 TRP A 436 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 3699) covalent geometry : angle 0.57703 / 0.28 ( 5030) SS BOND : bond 0.00151 / 0.07 ( 6) SS BOND : angle 0.42763 / 0.24 ( 12) hydrogen bonds : bond 0.02852 / 1.94 ( 79) hydrogen bonds : angle 5.67894 / 3.68 ( 204) link_BETA1-4 : bond 0.00594 / 0.31 ( 1) link_BETA1-4 : angle 1.50851 / 0.83 ( 3) link_NAG-ASN : bond 0.00214 / 0.10 ( 7) link_NAG-ASN : angle 3.13568 / 1.93 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.137 Fit side-chains REVERT: A 83 VAL cc_start: 0.7723 (OUTLIER) cc_final: 0.7504 (p) REVERT: A 129 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6131 (ptmm) REVERT: A 392 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: A 396 TYR cc_start: 0.7962 (m-80) cc_final: 0.7573 (m-10) REVERT: A 468 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8148 (tt) outliers start: 18 outliers final: 14 residues processed: 45 average time/residue: 0.0483 time to fit residues: 3.0247 Evaluate side-chains 47 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 29 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.158544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.123674 restraints weight = 5607.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.127699 restraints weight = 3775.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.130611 restraints weight = 2918.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.132684 restraints weight = 2440.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.133680 restraints weight = 2149.898| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3713 Z= 0.105 Angle : 0.589 8.874 5066 Z= 0.278 Chirality : 0.042 0.125 563 Planarity : 0.004 0.040 635 Dihedral : 4.860 37.509 657 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.74 % Favored : 90.02 % Rotamer: Outliers : 4.45 % Allowed : 23.82 % Favored : 71.73 % 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: -2.20 (0.41), residues: 421 helix: -0.33 (1.19), residues: 23 sheet: -0.98 (0.48), residues: 128 loop : -1.89 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.014 0.001 TYR A 265 PHE 0.015 0.001 PHE A 106 TRP 0.015 0.002 TRP A 436 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 3699) covalent geometry : angle 0.55922 / 0.27 ( 5030) SS BOND : bond 0.00156 / 0.07 ( 6) SS BOND : angle 0.35404 / 0.19 ( 12) hydrogen bonds : bond 0.02752 / 1.88 ( 79) hydrogen bonds : angle 5.69459 / 3.70 ( 204) link_BETA1-4 : bond 0.00488 / 0.26 ( 1) link_BETA1-4 : angle 1.45334 / 0.80 ( 3) link_NAG-ASN : bond 0.00206 / 0.10 ( 7) link_NAG-ASN : angle 2.92068 / 1.81 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 805.60 seconds wall clock time: 14 minutes 31.29 seconds (871.29 seconds total)