Starting phenix.real_space_refine on Wed Jul 1 20:44:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jzm_22533/07_2026/7jzm_22533.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzm_22533/07_2026/7jzm_22533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jzm_22533/07_2026/7jzm_22533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzm_22533/07_2026/7jzm_22533.map" model { file = "/net/cci-nas-00/data/ceres_data/7jzm_22533/07_2026/7jzm_22533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzm_22533/07_2026/7jzm_22533.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jzm_22533/07_2026/7jzm_22533.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jzm_22533/07_2026/7jzm_22533.cif" } resolution = 3.5 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= 0.022 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 10 5.16 5 C 1310 2.51 5 N 340 2.21 5 O 373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 2033 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 495 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1500 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.68, per 1000 atoms: 0.33 Number of scatterers: 2033 At special positions: 0 Unit cell: (66.15, 68.25, 69.3, 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 10 16.00 O 373 8.00 N 340 7.00 C 1310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.28 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 BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN B 343 " Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 45.8 milliseconds 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 38.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 Processing helix chain 'A' and resid 22 through 42 Processing helix chain 'A' and resid 44 through 64 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.804A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.514A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.158A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.670A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.479A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 93 hydrogen bonds defined for protein. 240 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: 0.16 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 591 1.33 - 1.46: 586 1.46 - 1.59: 893 1.59 - 1.72: 0 1.72 - 1.85: 12 Bond restraints: 2082 Sorted by residual: bond pdb=" N PRO B 499 " pdb=" CD PRO B 499 " ideal model delta sigma weight residual 1.473 1.337 0.136 1.40e-02 5.10e+03 9.45e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.479 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CG GLN B 506 " pdb=" CD GLN B 506 " ideal model delta sigma weight residual 1.516 1.438 0.078 2.50e-02 1.60e+03 9.74e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" C5 FUC C 3 " pdb=" O5 FUC C 3 " ideal model delta sigma weight residual 1.423 1.477 -0.054 2.00e-02 2.50e+03 7.29e+00 ... (remaining 2077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 2649 2.56 - 5.12: 157 5.12 - 7.69: 20 7.69 - 10.25: 3 10.25 - 12.81: 1 Bond angle restraints: 2830 Sorted by residual: angle pdb=" N PRO B 499 " pdb=" CA PRO B 499 " pdb=" CB PRO B 499 " ideal model delta sigma weight residual 103.41 96.76 6.65 9.40e-01 1.13e+00 5.01e+01 angle pdb=" CA PRO B 499 " pdb=" N PRO B 499 " pdb=" CD PRO B 499 " ideal model delta sigma weight residual 112.00 120.93 -8.93 1.40e+00 5.10e-01 4.07e+01 angle pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.56 126.01 -6.45 1.02e+00 9.61e-01 4.00e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.87 126.31 -6.44 1.04e+00 9.25e-01 3.84e+01 angle pdb=" C PHE B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 119.56 125.65 -6.09 1.01e+00 9.80e-01 3.64e+01 ... (remaining 2825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 1154 14.30 - 28.59: 45 28.59 - 42.89: 8 42.89 - 57.18: 5 57.18 - 71.48: 1 Dihedral angle restraints: 1213 sinusoidal: 454 harmonic: 759 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 51.36 41.64 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB GLU B 484 " pdb=" CG GLU B 484 " pdb=" CD GLU B 484 " pdb=" OE1 GLU B 484 " ideal model delta sinusoidal sigma weight residual 0.00 71.48 -71.48 1 3.00e+01 1.11e-03 7.28e+00 dihedral pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta harmonic sigma weight residual 180.00 166.92 13.08 0 5.00e+00 4.00e-02 6.85e+00 ... (remaining 1210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 230 0.082 - 0.164: 69 0.164 - 0.245: 15 0.245 - 0.327: 3 0.327 - 0.409: 1 Chirality restraints: 318 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.38e+01 chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.68e+01 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.90 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 315 not shown) Planarity restraints: 364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.036 2.00e-02 2.50e+03 1.86e-02 6.92e+00 pdb=" CG TYR B 495 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 453 " 0.025 2.00e-02 2.50e+03 1.34e-02 3.57e+00 pdb=" CG TYR B 453 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B 453 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 453 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 453 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 453 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 453 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 453 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.016 2.00e-02 2.50e+03 1.65e-02 3.40e+00 pdb=" CG ASN B 343 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.020 2.00e-02 2.50e+03 ... (remaining 361 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 880 2.92 - 3.41: 1816 3.41 - 3.91: 3445 3.91 - 4.40: 3881 4.40 - 4.90: 6261 Nonbonded interactions: 16283 Sorted by model distance: nonbonded pdb=" O ASP A 2 " pdb=" OD1 ASP A 2 " model vdw 2.420 3.040 nonbonded pdb=" N ASP B 428 " pdb=" OD1 ASP B 428 " model vdw 2.566 3.120 nonbonded pdb=" O ASN B 501 " pdb=" NE2 GLN B 506 " model vdw 2.568 3.120 nonbonded pdb=" O5 NAG C 1 " pdb=" O6 NAG C 1 " model vdw 2.569 2.432 nonbonded pdb=" N SER B 373 " pdb=" N PHE B 374 " model vdw 2.574 2.560 ... (remaining 16278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.020 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.016 0.245 2089 Z= 0.861 Angle : 1.414 12.996 2847 Z= 0.931 Chirality : 0.084 0.409 318 Planarity : 0.005 0.026 363 Dihedral : 9.289 71.478 715 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 0.75 (0.52), residues: 254 helix: 0.21 (0.51), residues: 85 sheet: 0.78 (0.76), residues: 52 loop : 0.82 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 355 TYR 0.036 0.006 TYR B 495 PHE 0.013 0.002 PHE B 342 TRP 0.012 0.005 TRP B 353 HIS 0.002 0.001 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.01477 / 0.81 ( 2082) covalent geometry : angle 1.37761 / 0.92 ( 2830) SS BOND : bond 0.12244 / 6.12 ( 4) SS BOND : angle 5.43319 / 3.63 ( 8) hydrogen bonds : bond 0.15984 / 10.02 ( 93) hydrogen bonds : angle 7.20776 / 5.17 ( 240) link_BETA1-4 : bond 0.07488 / 3.94 ( 1) link_BETA1-4 : angle 3.76318 / 2.11 ( 3) link_BETA1-6 : bond 0.05859 / 3.08 ( 1) link_BETA1-6 : angle 2.72093 / 1.46 ( 3) link_NAG-ASN : bond 0.05758 / 3.03 ( 1) link_NAG-ASN : angle 2.63632 / 1.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.052 Fit side-chains REVERT: B 469 SER cc_start: 0.8425 (t) cc_final: 0.7858 (p) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0767 time to fit residues: 5.7116 Evaluate side-chains 42 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 0.0870 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 6 optimal weight: 0.0050 overall best weight: 0.1972 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.130950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115235 restraints weight = 2964.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118201 restraints weight = 1576.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120266 restraints weight = 1053.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121619 restraints weight = 792.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122575 restraints weight = 649.811| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2089 Z= 0.160 Angle : 0.641 7.594 2847 Z= 0.338 Chirality : 0.044 0.145 318 Planarity : 0.004 0.039 363 Dihedral : 4.290 17.125 285 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.49 % Allowed : 9.95 % Favored : 87.56 % 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: 0.92 (0.53), residues: 254 helix: 1.01 (0.58), residues: 88 sheet: 0.51 (0.78), residues: 49 loop : 0.52 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 408 TYR 0.019 0.002 TYR B 495 PHE 0.016 0.002 PHE A 33 TRP 0.011 0.002 TRP B 436 HIS 0.002 0.001 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 2082) covalent geometry : angle 0.63279 / 0.34 ( 2830) SS BOND : bond 0.00628 / 0.31 ( 4) SS BOND : angle 1.63088 / 0.91 ( 8) hydrogen bonds : bond 0.05391 / 3.81 ( 93) hydrogen bonds : angle 5.26799 / 3.79 ( 240) link_BETA1-4 : bond 0.00298 / 0.16 ( 1) link_BETA1-4 : angle 1.29971 / 1.02 ( 3) link_BETA1-6 : bond 0.01038 / 0.55 ( 1) link_BETA1-6 : angle 1.54509 / 1.31 ( 3) link_NAG-ASN : bond 0.00108 / 0.06 ( 1) link_NAG-ASN : angle 1.26928 / 0.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 25 ILE cc_start: 0.8288 (mm) cc_final: 0.7863 (mt) outliers start: 5 outliers final: 2 residues processed: 40 average time/residue: 0.0535 time to fit residues: 2.5716 Evaluate side-chains 38 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 23 optimal weight: 0.1980 chunk 9 optimal weight: 0.0270 chunk 7 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 overall best weight: 0.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 HIS A 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111701 restraints weight = 3039.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114634 restraints weight = 1663.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116590 restraints weight = 1120.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117729 restraints weight = 855.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118706 restraints weight = 722.168| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2089 Z= 0.162 Angle : 0.584 5.968 2847 Z= 0.302 Chirality : 0.042 0.137 318 Planarity : 0.004 0.040 363 Dihedral : 4.202 17.711 285 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.99 % Allowed : 7.96 % Favored : 89.05 % 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: 0.68 (0.53), residues: 254 helix: 1.06 (0.57), residues: 89 sheet: -0.02 (0.75), residues: 49 loop : 0.37 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 45 TYR 0.016 0.002 TYR B 495 PHE 0.008 0.001 PHE A 33 TRP 0.009 0.002 TRP B 436 HIS 0.002 0.001 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 2082) covalent geometry : angle 0.57656 / 0.30 ( 2830) SS BOND : bond 0.00538 / 0.27 ( 4) SS BOND : angle 1.38626 / 0.78 ( 8) hydrogen bonds : bond 0.04567 / 3.19 ( 93) hydrogen bonds : angle 5.04178 / 3.62 ( 240) link_BETA1-4 : bond 0.00410 / 0.22 ( 1) link_BETA1-4 : angle 0.92608 / 0.65 ( 3) link_BETA1-6 : bond 0.00890 / 0.47 ( 1) link_BETA1-6 : angle 1.56451 / 1.33 ( 3) link_NAG-ASN : bond 0.00028 / 0.01 ( 1) link_NAG-ASN : angle 1.25951 / 0.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.080 Fit side-chains REVERT: A 25 ILE cc_start: 0.8399 (mm) cc_final: 0.8023 (mt) REVERT: A 34 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: B 489 TYR cc_start: 0.7909 (m-80) cc_final: 0.7318 (m-80) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.0517 time to fit residues: 2.7352 Evaluate side-chains 41 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 15 optimal weight: 0.0170 chunk 4 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 18 optimal weight: 0.4980 chunk 23 optimal weight: 0.0970 chunk 19 optimal weight: 0.4980 chunk 9 optimal weight: 0.0470 overall best weight: 0.0712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114691 restraints weight = 2964.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117669 restraints weight = 1643.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119657 restraints weight = 1109.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120993 restraints weight = 848.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121892 restraints weight = 701.352| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2089 Z= 0.095 Angle : 0.531 6.594 2847 Z= 0.266 Chirality : 0.041 0.131 318 Planarity : 0.003 0.040 363 Dihedral : 3.910 16.291 285 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.99 % Allowed : 10.95 % Favored : 87.06 % 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: 0.71 (0.52), residues: 254 helix: 1.20 (0.57), residues: 88 sheet: -0.10 (0.74), residues: 49 loop : 0.33 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 45 TYR 0.009 0.001 TYR B 495 PHE 0.011 0.001 PHE A 33 TRP 0.009 0.001 TRP B 436 HIS 0.000 0.000 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 ( 2082) covalent geometry : angle 0.52468 / 0.26 ( 2830) SS BOND : bond 0.00616 / 0.32 ( 4) SS BOND : angle 1.24687 / 0.70 ( 8) hydrogen bonds : bond 0.03636 / 2.57 ( 93) hydrogen bonds : angle 4.73201 / 3.43 ( 240) link_BETA1-4 : bond 0.00358 / 0.19 ( 1) link_BETA1-4 : angle 0.94500 / 0.75 ( 3) link_BETA1-6 : bond 0.00745 / 0.39 ( 1) link_BETA1-6 : angle 1.26476 / 1.12 ( 3) link_NAG-ASN : bond 0.00109 / 0.06 ( 1) link_NAG-ASN : angle 1.07113 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.066 Fit side-chains REVERT: A 25 ILE cc_start: 0.8401 (mm) cc_final: 0.8066 (mt) REVERT: A 34 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: B 489 TYR cc_start: 0.7639 (m-80) cc_final: 0.6779 (m-80) outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.0579 time to fit residues: 3.0806 Evaluate side-chains 41 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 0.2980 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 6 optimal weight: 0.1980 chunk 13 optimal weight: 0.0270 chunk 18 optimal weight: 0.2980 chunk 22 optimal weight: 0.2980 chunk 3 optimal weight: 0.2980 chunk 10 optimal weight: 0.0670 chunk 23 optimal weight: 0.0970 overall best weight: 0.1374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112924 restraints weight = 3025.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115752 restraints weight = 1697.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117693 restraints weight = 1155.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118848 restraints weight = 888.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119703 restraints weight = 750.317| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2089 Z= 0.118 Angle : 0.544 6.843 2847 Z= 0.277 Chirality : 0.042 0.132 318 Planarity : 0.004 0.041 363 Dihedral : 3.930 17.339 285 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.99 % Allowed : 12.94 % Favored : 85.07 % 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: 0.78 (0.54), residues: 254 helix: 1.19 (0.57), residues: 88 sheet: -0.13 (0.75), residues: 49 loop : 0.46 (0.59), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.010 0.001 TYR B 495 PHE 0.010 0.001 PHE A 33 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 2082) covalent geometry : angle 0.53788 / 0.27 ( 2830) SS BOND : bond 0.00237 / 0.12 ( 4) SS BOND : angle 1.27216 / 0.74 ( 8) hydrogen bonds : bond 0.03738 / 2.62 ( 93) hydrogen bonds : angle 4.71330 / 3.39 ( 240) link_BETA1-4 : bond 0.00243 / 0.13 ( 1) link_BETA1-4 : angle 0.85327 / 0.65 ( 3) link_BETA1-6 : bond 0.00771 / 0.41 ( 1) link_BETA1-6 : angle 1.35340 / 1.19 ( 3) link_NAG-ASN : bond 0.00077 / 0.04 ( 1) link_NAG-ASN : angle 1.10546 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.077 Fit side-chains REVERT: A 9 MET cc_start: 0.7802 (tmm) cc_final: 0.7509 (ttt) REVERT: A 25 ILE cc_start: 0.8488 (mm) cc_final: 0.8102 (mt) REVERT: A 34 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: B 489 TYR cc_start: 0.7635 (m-80) cc_final: 0.6726 (m-80) outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.0600 time to fit residues: 2.7922 Evaluate side-chains 38 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.0030 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 9 optimal weight: 0.3980 chunk 2 optimal weight: 0.0980 chunk 20 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 4 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 overall best weight: 0.1988 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.128058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111586 restraints weight = 2942.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114373 restraints weight = 1642.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116294 restraints weight = 1117.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117540 restraints weight = 861.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118311 restraints weight = 717.730| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2089 Z= 0.136 Angle : 0.548 6.822 2847 Z= 0.278 Chirality : 0.042 0.131 318 Planarity : 0.004 0.044 363 Dihedral : 3.980 17.448 285 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.99 % Allowed : 13.93 % Favored : 83.08 % 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: 0.72 (0.54), residues: 254 helix: 1.28 (0.58), residues: 88 sheet: -0.23 (0.76), residues: 49 loop : 0.35 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.010 0.001 TYR B 495 PHE 0.010 0.001 PHE A 33 TRP 0.009 0.001 TRP B 436 HIS 0.001 0.001 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 2082) covalent geometry : angle 0.54221 / 0.28 ( 2830) SS BOND : bond 0.00305 / 0.15 ( 4) SS BOND : angle 1.19170 / 0.70 ( 8) hydrogen bonds : bond 0.03655 / 2.54 ( 93) hydrogen bonds : angle 4.68094 / 3.37 ( 240) link_BETA1-4 : bond 0.00344 / 0.18 ( 1) link_BETA1-4 : angle 0.89720 / 0.69 ( 3) link_BETA1-6 : bond 0.00860 / 0.45 ( 1) link_BETA1-6 : angle 1.43733 / 1.25 ( 3) link_NAG-ASN : bond 0.00026 / 0.01 ( 1) link_NAG-ASN : angle 1.22897 / 0.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.084 Fit side-chains REVERT: A 25 ILE cc_start: 0.8602 (mm) cc_final: 0.8229 (mt) REVERT: A 34 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: B 489 TYR cc_start: 0.7620 (m-80) cc_final: 0.6449 (m-80) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.0594 time to fit residues: 2.6313 Evaluate side-chains 39 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 9 optimal weight: 0.0040 chunk 7 optimal weight: 0.2980 chunk 0 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 18 optimal weight: 0.0980 overall best weight: 0.2192 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.127397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110769 restraints weight = 3045.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113681 restraints weight = 1697.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115608 restraints weight = 1148.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116825 restraints weight = 880.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117441 restraints weight = 736.581| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2089 Z= 0.146 Angle : 0.624 11.154 2847 Z= 0.301 Chirality : 0.042 0.131 318 Planarity : 0.004 0.044 363 Dihedral : 4.081 17.017 285 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.99 % Allowed : 14.93 % Favored : 82.09 % 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: 0.53 (0.53), residues: 254 helix: 1.14 (0.58), residues: 88 sheet: -0.29 (0.77), residues: 49 loop : 0.19 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.010 0.001 TYR B 495 PHE 0.009 0.001 PHE B 464 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.001 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 2082) covalent geometry : angle 0.61868 / 0.30 ( 2830) SS BOND : bond 0.00266 / 0.13 ( 4) SS BOND : angle 1.17425 / 0.69 ( 8) hydrogen bonds : bond 0.03622 / 2.49 ( 93) hydrogen bonds : angle 4.71738 / 3.39 ( 240) link_BETA1-4 : bond 0.00361 / 0.19 ( 1) link_BETA1-4 : angle 0.89025 / 0.67 ( 3) link_BETA1-6 : bond 0.00670 / 0.35 ( 1) link_BETA1-6 : angle 1.43533 / 1.22 ( 3) link_NAG-ASN : bond 0.00018 / 0.01 ( 1) link_NAG-ASN : angle 1.32991 / 0.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.075 Fit side-chains REVERT: A 25 ILE cc_start: 0.8603 (mm) cc_final: 0.8223 (mt) REVERT: A 34 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: B 474 GLN cc_start: 0.7774 (tp40) cc_final: 0.7560 (tp40) REVERT: B 489 TYR cc_start: 0.7579 (m-80) cc_final: 0.6391 (m-80) outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 0.0572 time to fit residues: 2.5339 Evaluate side-chains 40 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 0.4980 chunk 10 optimal weight: 0.3980 chunk 5 optimal weight: 0.2980 chunk 20 optimal weight: 0.0470 chunk 11 optimal weight: 0.2980 overall best weight: 0.2278 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.126886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110392 restraints weight = 2994.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.113294 restraints weight = 1670.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115179 restraints weight = 1131.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116354 restraints weight = 869.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117304 restraints weight = 729.202| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2089 Z= 0.148 Angle : 0.604 9.869 2847 Z= 0.293 Chirality : 0.043 0.131 318 Planarity : 0.004 0.044 363 Dihedral : 4.246 18.692 285 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.49 % Allowed : 15.92 % Favored : 81.59 % 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: 0.47 (0.54), residues: 254 helix: 1.18 (0.58), residues: 88 sheet: -0.38 (0.78), residues: 49 loop : 0.10 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.011 0.001 TYR B 495 PHE 0.009 0.001 PHE B 464 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 2082) covalent geometry : angle 0.59778 / 0.29 ( 2830) SS BOND : bond 0.00233 / 0.12 ( 4) SS BOND : angle 1.22105 / 0.71 ( 8) hydrogen bonds : bond 0.03608 / 2.46 ( 93) hydrogen bonds : angle 4.71767 / 3.39 ( 240) link_BETA1-4 : bond 0.00340 / 0.18 ( 1) link_BETA1-4 : angle 0.87533 / 0.63 ( 3) link_BETA1-6 : bond 0.00681 / 0.36 ( 1) link_BETA1-6 : angle 1.43619 / 1.22 ( 3) link_NAG-ASN : bond 0.00023 / 0.01 ( 1) link_NAG-ASN : angle 1.40215 / 0.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.7929 (tmm) cc_final: 0.7569 (ttp) REVERT: A 25 ILE cc_start: 0.8663 (mm) cc_final: 0.8282 (mt) REVERT: A 34 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: B 474 GLN cc_start: 0.7681 (tp40) cc_final: 0.7445 (tp40) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.0657 time to fit residues: 3.0813 Evaluate side-chains 40 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 18 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.0670 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 14 optimal weight: 0.3980 chunk 24 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 11 optimal weight: 0.0980 overall best weight: 0.2118 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.126866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110645 restraints weight = 2933.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113352 restraints weight = 1691.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115233 restraints weight = 1171.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116430 restraints weight = 906.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116861 restraints weight = 763.714| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2089 Z= 0.139 Angle : 0.599 9.969 2847 Z= 0.289 Chirality : 0.042 0.131 318 Planarity : 0.004 0.046 363 Dihedral : 4.207 17.585 285 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.99 % Allowed : 15.92 % Favored : 81.09 % 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: 0.42 (0.54), residues: 254 helix: 1.11 (0.58), residues: 89 sheet: -0.38 (0.80), residues: 49 loop : 0.08 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.010 0.001 TYR B 495 PHE 0.009 0.001 PHE B 464 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 2082) covalent geometry : angle 0.59274 / 0.29 ( 2830) SS BOND : bond 0.00226 / 0.11 ( 4) SS BOND : angle 1.22744 / 0.72 ( 8) hydrogen bonds : bond 0.03504 / 2.38 ( 93) hydrogen bonds : angle 4.69694 / 3.38 ( 240) link_BETA1-4 : bond 0.00352 / 0.19 ( 1) link_BETA1-4 : angle 0.86293 / 0.62 ( 3) link_BETA1-6 : bond 0.00712 / 0.37 ( 1) link_BETA1-6 : angle 1.39369 / 1.20 ( 3) link_NAG-ASN : bond 0.00019 / 0.01 ( 1) link_NAG-ASN : angle 1.42136 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.7812 (tmm) cc_final: 0.7489 (ttt) REVERT: A 25 ILE cc_start: 0.8575 (mm) cc_final: 0.8219 (mt) outliers start: 6 outliers final: 6 residues processed: 36 average time/residue: 0.0571 time to fit residues: 2.4661 Evaluate side-chains 37 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 0.3980 chunk 23 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 8 optimal weight: 0.0970 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 0.4980 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110343 restraints weight = 2998.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113162 restraints weight = 1682.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114903 restraints weight = 1150.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116230 restraints weight = 898.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117153 restraints weight = 750.435| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2089 Z= 0.136 Angle : 0.601 9.354 2847 Z= 0.296 Chirality : 0.043 0.130 318 Planarity : 0.004 0.046 363 Dihedral : 4.232 17.639 285 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.99 % Allowed : 15.92 % Favored : 81.09 % 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: 0.41 (0.54), residues: 254 helix: 1.11 (0.58), residues: 88 sheet: -0.36 (0.80), residues: 49 loop : 0.06 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.009 0.001 TYR B 495 PHE 0.006 0.001 PHE B 464 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 2082) covalent geometry : angle 0.59533 / 0.29 ( 2830) SS BOND : bond 0.00223 / 0.11 ( 4) SS BOND : angle 1.20410 / 0.70 ( 8) hydrogen bonds : bond 0.03559 / 2.42 ( 93) hydrogen bonds : angle 4.74889 / 3.42 ( 240) link_BETA1-4 : bond 0.00328 / 0.17 ( 1) link_BETA1-4 : angle 0.85363 / 0.61 ( 3) link_BETA1-6 : bond 0.00617 / 0.32 ( 1) link_BETA1-6 : angle 1.33300 / 1.14 ( 3) link_NAG-ASN : bond 0.00014 / 0.01 ( 1) link_NAG-ASN : angle 1.41538 / 0.84 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.048 Fit side-chains REVERT: A 9 MET cc_start: 0.7813 (tmm) cc_final: 0.7523 (ttt) REVERT: A 25 ILE cc_start: 0.8603 (mm) cc_final: 0.8249 (mt) outliers start: 6 outliers final: 5 residues processed: 34 average time/residue: 0.0543 time to fit residues: 2.2034 Evaluate side-chains 36 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.2980 chunk 2 optimal weight: 0.0970 chunk 7 optimal weight: 0.0060 chunk 3 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.0670 chunk 6 optimal weight: 0.0670 chunk 14 optimal weight: 0.6980 overall best weight: 0.0670 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.129604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113092 restraints weight = 3032.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116057 restraints weight = 1662.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118019 restraints weight = 1118.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119175 restraints weight = 852.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120156 restraints weight = 715.423| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2089 Z= 0.101 Angle : 0.604 9.774 2847 Z= 0.290 Chirality : 0.041 0.127 318 Planarity : 0.004 0.045 363 Dihedral : 4.073 17.736 285 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.99 % Allowed : 16.42 % Favored : 81.59 % 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: 0.61 (0.55), residues: 254 helix: 1.27 (0.58), residues: 88 sheet: -0.14 (0.85), residues: 47 loop : 0.11 (0.58), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.008 0.001 TYR A 14 PHE 0.011 0.001 PHE A 33 TRP 0.009 0.001 TRP B 436 HIS 0.000 0.000 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 2082) covalent geometry : angle 0.59993 / 0.29 ( 2830) SS BOND : bond 0.00252 / 0.13 ( 4) SS BOND : angle 1.17700 / 0.67 ( 8) hydrogen bonds : bond 0.03185 / 2.17 ( 93) hydrogen bonds : angle 4.58487 / 3.33 ( 240) link_BETA1-4 : bond 0.00357 / 0.19 ( 1) link_BETA1-4 : angle 0.82091 / 0.64 ( 3) link_BETA1-6 : bond 0.00641 / 0.34 ( 1) link_BETA1-6 : angle 1.16694 / 1.03 ( 3) link_NAG-ASN : bond 0.00112 / 0.06 ( 1) link_NAG-ASN : angle 1.15380 / 0.72 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 779.52 seconds wall clock time: 14 minutes 13.80 seconds (853.80 seconds total)