Starting phenix.real_space_refine on Tue Mar 3 11:37:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wry_32737/03_2026/7wry_32737.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wry_32737/03_2026/7wry_32737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wry_32737/03_2026/7wry_32737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wry_32737/03_2026/7wry_32737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wry_32737/03_2026/7wry_32737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wry_32737/03_2026/7wry_32737.map" } resolution = 3.28 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= 0.055 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 14 5.16 5 C 2078 2.51 5 N 549 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3267 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1496 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain breaks: 1 Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 930 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.93, per 1000 atoms: 0.28 Number of scatterers: 3267 At special positions: 0 Unit cell: (76.68, 81, 73.44, 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 14 16.00 O 626 8.00 N 549 7.00 C 2078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.06 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 123.8 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 10.7% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 337 through 341 removed outlier: 3.706A pdb=" N GLU R 340 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 387 Processing helix chain 'R' and resid 405 through 410 removed outlier: 5.153A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 422 removed outlier: 3.787A pdb=" N TYR R 421 " --> pdb=" O LYS R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.910A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.677A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.541A pdb=" N ASP H 90 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR H 91 " --> pdb=" O ILE H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'R' and resid 356 through 358 removed outlier: 3.636A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.702A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.540A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.273A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.685A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.628A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.948A pdb=" N ALA H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.948A pdb=" N ALA H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 201 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: 0.47 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 1042 1.36 - 1.49: 972 1.49 - 1.62: 1320 1.62 - 1.75: 0 1.75 - 1.88: 16 Bond restraints: 3350 Sorted by residual: bond pdb=" C LYS R 478 " pdb=" N PRO R 479 " ideal model delta sigma weight residual 1.332 1.360 -0.029 1.26e-02 6.30e+03 5.21e+00 bond pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 1.808 1.882 -0.074 3.30e-02 9.18e+02 5.05e+00 bond pdb=" N ASN R 487 " pdb=" CA ASN R 487 " ideal model delta sigma weight residual 1.462 1.486 -0.025 1.48e-02 4.57e+03 2.81e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 3345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 4464 2.78 - 5.55: 79 5.55 - 8.33: 9 8.33 - 11.11: 3 11.11 - 13.88: 1 Bond angle restraints: 4556 Sorted by residual: angle pdb=" C TYR R 473 " pdb=" N GLN R 474 " pdb=" CA GLN R 474 " ideal model delta sigma weight residual 120.82 130.37 -9.55 1.50e+00 4.44e-01 4.05e+01 angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 128.28 -13.88 2.30e+00 1.89e-01 3.64e+01 angle pdb=" C PHE R 486 " pdb=" N ASN R 487 " pdb=" CA ASN R 487 " ideal model delta sigma weight residual 122.61 131.45 -8.84 1.56e+00 4.11e-01 3.21e+01 angle pdb=" N GLY L 50 " pdb=" CA GLY L 50 " pdb=" C GLY L 50 " ideal model delta sigma weight residual 111.14 103.18 7.96 1.46e+00 4.69e-01 2.97e+01 angle pdb=" N GLN R 474 " pdb=" CA GLN R 474 " pdb=" C GLN R 474 " ideal model delta sigma weight residual 111.37 118.99 -7.62 1.65e+00 3.67e-01 2.13e+01 ... (remaining 4551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 1831 21.36 - 42.72: 136 42.72 - 64.08: 14 64.08 - 85.44: 12 85.44 - 106.80: 5 Dihedral angle restraints: 1998 sinusoidal: 808 harmonic: 1190 Sorted by residual: dihedral pdb=" CA TYR R 473 " pdb=" C TYR R 473 " pdb=" N GLN R 474 " pdb=" CA GLN R 474 " ideal model delta harmonic sigma weight residual 180.00 -143.17 -36.83 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.29 48.71 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CA GLY L 50 " pdb=" C GLY L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta harmonic sigma weight residual 180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 1995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 394 0.058 - 0.115: 82 0.115 - 0.172: 16 0.172 - 0.229: 4 0.229 - 0.287: 3 Chirality restraints: 499 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ASN R 487 " pdb=" N ASN R 487 " pdb=" C ASN R 487 " pdb=" CB ASN R 487 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLN R 474 " pdb=" N GLN R 474 " pdb=" C GLN R 474 " pdb=" CB GLN R 474 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 496 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO L 59 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 14 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO L 15 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 486 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C PHE R 486 " -0.033 2.00e-02 2.50e+03 pdb=" O PHE R 486 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN R 487 " 0.011 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1026 2.83 - 3.35: 2557 3.35 - 3.87: 5385 3.87 - 4.38: 6325 4.38 - 4.90: 10971 Nonbonded interactions: 26264 Sorted by model distance: nonbonded pdb=" OD1 ASP R 442 " pdb=" OH TYR H 103 " model vdw 2.313 3.040 nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.323 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.333 3.040 nonbonded pdb=" OG SER L 65 " pdb=" OG1 THR L 72 " model vdw 2.342 3.040 nonbonded pdb=" OE1 GLU R 406 " pdb=" OH TYR R 495 " model vdw 2.356 3.040 ... (remaining 26259 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.260 Find NCS groups from input model: 0.020 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 : 0.006 0.074 3359 Z= 0.258 Angle : 0.929 13.884 4577 Z= 0.516 Chirality : 0.056 0.287 499 Planarity : 0.007 0.068 584 Dihedral : 16.465 106.799 1226 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.29 % Allowed : 0.00 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.76 (0.38), residues: 405 helix: -4.91 (0.29), residues: 27 sheet: -1.33 (0.40), residues: 152 loop : -1.77 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG R 457 TYR 0.024 0.002 TYR H 27 PHE 0.029 0.002 PHE R 377 TRP 0.011 0.002 TRP H 47 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 3350) covalent geometry : angle 0.91472 ( 4556) SS BOND : bond 0.01206 ( 6) SS BOND : angle 2.44374 ( 12) hydrogen bonds : bond 0.27476 ( 81) hydrogen bonds : angle 9.91062 ( 201) link_BETA1-4 : bond 0.00480 ( 2) link_BETA1-4 : angle 2.40944 ( 6) link_NAG-ASN : bond 0.00354 ( 1) link_NAG-ASN : angle 3.38041 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.144 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.0703 time to fit residues: 6.3141 Evaluate side-chains 70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 27 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103923 restraints weight = 4610.823| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.94 r_work: 0.3009 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3359 Z= 0.236 Angle : 0.679 8.303 4577 Z= 0.355 Chirality : 0.047 0.150 499 Planarity : 0.006 0.052 584 Dihedral : 9.740 67.469 517 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.86 % Allowed : 11.78 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -2.38 (0.38), residues: 405 helix: -4.42 (0.52), residues: 27 sheet: -0.98 (0.42), residues: 148 loop : -1.61 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 457 TYR 0.021 0.002 TYR H 27 PHE 0.009 0.001 PHE R 456 TRP 0.012 0.002 TRP H 47 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 3350) covalent geometry : angle 0.66236 ( 4556) SS BOND : bond 0.00798 ( 6) SS BOND : angle 1.79865 ( 12) hydrogen bonds : bond 0.05596 ( 81) hydrogen bonds : angle 6.88104 ( 201) link_BETA1-4 : bond 0.00338 ( 2) link_BETA1-4 : angle 2.50029 ( 6) link_NAG-ASN : bond 0.00163 ( 1) link_NAG-ASN : angle 3.29937 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.146 Fit side-chains REVERT: H 23 LYS cc_start: 0.8578 (tttp) cc_final: 0.8303 (tttp) REVERT: H 82 GLN cc_start: 0.7598 (mm110) cc_final: 0.7245 (mm-40) REVERT: H 104 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8359 (mm-30) outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 0.0691 time to fit residues: 6.0988 Evaluate side-chains 70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.104572 restraints weight = 4652.564| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.16 r_work: 0.3021 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3359 Z= 0.159 Angle : 0.586 7.200 4577 Z= 0.306 Chirality : 0.045 0.146 499 Planarity : 0.005 0.047 584 Dihedral : 6.453 35.092 517 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.72 % Allowed : 14.37 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -2.03 (0.39), residues: 405 helix: -4.24 (0.59), residues: 27 sheet: -0.68 (0.44), residues: 137 loop : -1.40 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 457 TYR 0.018 0.001 TYR H 27 PHE 0.009 0.001 PHE R 456 TRP 0.010 0.001 TRP R 436 HIS 0.002 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3350) covalent geometry : angle 0.56985 ( 4556) SS BOND : bond 0.00695 ( 6) SS BOND : angle 1.51376 ( 12) hydrogen bonds : bond 0.03833 ( 81) hydrogen bonds : angle 6.09496 ( 201) link_BETA1-4 : bond 0.00452 ( 2) link_BETA1-4 : angle 2.41926 ( 6) link_NAG-ASN : bond 0.00054 ( 1) link_NAG-ASN : angle 3.21545 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.129 Fit side-chains REVERT: L 48 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8329 (mp) REVERT: H 3 GLN cc_start: 0.7681 (mt0) cc_final: 0.7301 (pt0) REVERT: H 23 LYS cc_start: 0.8579 (tttp) cc_final: 0.8265 (tttp) REVERT: H 82 GLN cc_start: 0.7904 (mm110) cc_final: 0.7358 (mm-40) REVERT: H 89 GLU cc_start: 0.8894 (pm20) cc_final: 0.8545 (pm20) outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 0.0758 time to fit residues: 6.4485 Evaluate side-chains 69 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.104592 restraints weight = 4694.947| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.16 r_work: 0.3021 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3359 Z= 0.158 Angle : 0.567 7.188 4577 Z= 0.298 Chirality : 0.044 0.144 499 Planarity : 0.004 0.045 584 Dihedral : 4.997 22.217 517 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.72 % Allowed : 14.37 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.79 (0.40), residues: 405 helix: -4.17 (0.61), residues: 27 sheet: -0.47 (0.44), residues: 137 loop : -1.26 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 457 TYR 0.009 0.001 TYR L 91 PHE 0.010 0.001 PHE R 456 TRP 0.009 0.001 TRP R 436 HIS 0.002 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3350) covalent geometry : angle 0.55283 ( 4556) SS BOND : bond 0.00620 ( 6) SS BOND : angle 1.44970 ( 12) hydrogen bonds : bond 0.03472 ( 81) hydrogen bonds : angle 5.72286 ( 201) link_BETA1-4 : bond 0.00404 ( 2) link_BETA1-4 : angle 2.04191 ( 6) link_NAG-ASN : bond 0.00181 ( 1) link_NAG-ASN : angle 3.19298 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.126 Fit side-chains REVERT: L 48 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8306 (mp) REVERT: H 23 LYS cc_start: 0.8547 (tttp) cc_final: 0.8246 (tttp) REVERT: H 82 GLN cc_start: 0.7816 (mm110) cc_final: 0.7400 (mm-40) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.0714 time to fit residues: 6.0730 Evaluate side-chains 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 65 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 20 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.107626 restraints weight = 4610.288| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.14 r_work: 0.3058 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3359 Z= 0.107 Angle : 0.518 6.001 4577 Z= 0.273 Chirality : 0.043 0.148 499 Planarity : 0.004 0.043 584 Dihedral : 4.650 19.145 517 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.01 % Allowed : 14.94 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.47 (0.41), residues: 405 helix: -4.51 (0.53), residues: 21 sheet: -0.33 (0.45), residues: 137 loop : -1.01 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.017 0.001 TYR H 27 PHE 0.005 0.001 PHE R 456 TRP 0.011 0.001 TRP R 436 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3350) covalent geometry : angle 0.50504 ( 4556) SS BOND : bond 0.00565 ( 6) SS BOND : angle 1.26922 ( 12) hydrogen bonds : bond 0.02960 ( 81) hydrogen bonds : angle 5.43880 ( 201) link_BETA1-4 : bond 0.00377 ( 2) link_BETA1-4 : angle 1.63582 ( 6) link_NAG-ASN : bond 0.00088 ( 1) link_NAG-ASN : angle 3.17355 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.123 Fit side-chains REVERT: L 48 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8347 (mp) REVERT: H 23 LYS cc_start: 0.8488 (tttp) cc_final: 0.8194 (tttp) REVERT: H 82 GLN cc_start: 0.7720 (mm110) cc_final: 0.7449 (mm110) outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.0654 time to fit residues: 5.8962 Evaluate side-chains 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.0010 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 overall best weight: 0.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.110016 restraints weight = 4676.383| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.21 r_work: 0.3094 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3359 Z= 0.090 Angle : 0.508 5.232 4577 Z= 0.267 Chirality : 0.042 0.144 499 Planarity : 0.004 0.042 584 Dihedral : 4.302 19.350 517 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.72 % Allowed : 16.38 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.25 (0.42), residues: 405 helix: -4.37 (0.60), residues: 21 sheet: -0.14 (0.46), residues: 136 loop : -0.88 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.007 0.001 TYR H 103 PHE 0.005 0.001 PHE H 70 TRP 0.010 0.001 TRP R 436 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 3350) covalent geometry : angle 0.49636 ( 4556) SS BOND : bond 0.00473 ( 6) SS BOND : angle 1.15912 ( 12) hydrogen bonds : bond 0.02692 ( 81) hydrogen bonds : angle 5.16066 ( 201) link_BETA1-4 : bond 0.00387 ( 2) link_BETA1-4 : angle 1.48899 ( 6) link_NAG-ASN : bond 0.00025 ( 1) link_NAG-ASN : angle 3.08469 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.096 Fit side-chains REVERT: L 48 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8429 (mp) REVERT: H 23 LYS cc_start: 0.8435 (tttp) cc_final: 0.8216 (tttm) REVERT: H 82 GLN cc_start: 0.7757 (mm110) cc_final: 0.7498 (mm110) REVERT: H 95 TYR cc_start: 0.8918 (m-80) cc_final: 0.8670 (m-80) REVERT: H 101 ASP cc_start: 0.8117 (t70) cc_final: 0.7850 (t70) outliers start: 6 outliers final: 5 residues processed: 73 average time/residue: 0.0673 time to fit residues: 6.0762 Evaluate side-chains 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 32 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.108141 restraints weight = 4721.881| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.20 r_work: 0.3073 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3359 Z= 0.115 Angle : 0.525 5.838 4577 Z= 0.273 Chirality : 0.043 0.147 499 Planarity : 0.004 0.040 584 Dihedral : 4.276 18.844 517 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.30 % Allowed : 15.23 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.20 (0.42), residues: 405 helix: -4.32 (0.63), residues: 21 sheet: -0.27 (0.44), residues: 148 loop : -0.76 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 457 TYR 0.019 0.001 TYR H 27 PHE 0.004 0.001 PHE R 456 TRP 0.007 0.001 TRP R 436 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3350) covalent geometry : angle 0.51393 ( 4556) SS BOND : bond 0.00485 ( 6) SS BOND : angle 1.22014 ( 12) hydrogen bonds : bond 0.02812 ( 81) hydrogen bonds : angle 5.14758 ( 201) link_BETA1-4 : bond 0.00364 ( 2) link_BETA1-4 : angle 1.46764 ( 6) link_NAG-ASN : bond 0.00154 ( 1) link_NAG-ASN : angle 3.00759 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.140 Fit side-chains REVERT: L 48 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8464 (mp) REVERT: H 23 LYS cc_start: 0.8470 (tttp) cc_final: 0.8225 (tttm) REVERT: H 82 GLN cc_start: 0.7736 (mm110) cc_final: 0.7479 (mm110) REVERT: H 101 ASP cc_start: 0.8156 (t70) cc_final: 0.7903 (t70) outliers start: 8 outliers final: 6 residues processed: 75 average time/residue: 0.0682 time to fit residues: 6.2711 Evaluate side-chains 78 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.105563 restraints weight = 4829.074| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.22 r_work: 0.3036 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3359 Z= 0.149 Angle : 0.568 8.075 4577 Z= 0.290 Chirality : 0.043 0.145 499 Planarity : 0.004 0.040 584 Dihedral : 4.458 18.695 517 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.01 % Allowed : 16.38 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.38 (0.42), residues: 405 helix: -3.99 (0.65), residues: 27 sheet: -0.29 (0.44), residues: 148 loop : -0.90 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.009 0.001 TYR H 103 PHE 0.005 0.001 PHE R 456 TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3350) covalent geometry : angle 0.55529 ( 4556) SS BOND : bond 0.00569 ( 6) SS BOND : angle 1.58201 ( 12) hydrogen bonds : bond 0.02983 ( 81) hydrogen bonds : angle 5.17379 ( 201) link_BETA1-4 : bond 0.00334 ( 2) link_BETA1-4 : angle 1.46736 ( 6) link_NAG-ASN : bond 0.00291 ( 1) link_NAG-ASN : angle 3.02602 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.124 Fit side-chains REVERT: L 48 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8396 (mp) REVERT: H 23 LYS cc_start: 0.8496 (tttp) cc_final: 0.8250 (tttm) REVERT: H 82 GLN cc_start: 0.7737 (mm110) cc_final: 0.7511 (mm110) REVERT: H 101 ASP cc_start: 0.8211 (t70) cc_final: 0.7983 (t70) outliers start: 7 outliers final: 6 residues processed: 74 average time/residue: 0.0687 time to fit residues: 6.1756 Evaluate side-chains 75 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.0000 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.105450 restraints weight = 4752.949| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.20 r_work: 0.3035 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3359 Z= 0.147 Angle : 0.547 5.878 4577 Z= 0.285 Chirality : 0.043 0.147 499 Planarity : 0.004 0.040 584 Dihedral : 4.482 19.488 517 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.01 % Allowed : 16.95 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.34 (0.42), residues: 405 helix: -3.99 (0.65), residues: 27 sheet: -0.24 (0.44), residues: 148 loop : -0.89 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.019 0.001 TYR H 27 PHE 0.004 0.001 PHE R 456 TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3350) covalent geometry : angle 0.53471 ( 4556) SS BOND : bond 0.00557 ( 6) SS BOND : angle 1.56947 ( 12) hydrogen bonds : bond 0.02929 ( 81) hydrogen bonds : angle 5.16830 ( 201) link_BETA1-4 : bond 0.00320 ( 2) link_BETA1-4 : angle 1.43718 ( 6) link_NAG-ASN : bond 0.00281 ( 1) link_NAG-ASN : angle 3.01386 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.128 Fit side-chains REVERT: L 48 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8338 (mp) REVERT: H 23 LYS cc_start: 0.8469 (tttp) cc_final: 0.8213 (tttm) REVERT: H 82 GLN cc_start: 0.7710 (mm110) cc_final: 0.7480 (mm110) REVERT: H 101 ASP cc_start: 0.8240 (t70) cc_final: 0.8017 (t70) outliers start: 7 outliers final: 6 residues processed: 74 average time/residue: 0.0733 time to fit residues: 6.6111 Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.105455 restraints weight = 4729.448| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.20 r_work: 0.3034 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3359 Z= 0.145 Angle : 0.546 5.913 4577 Z= 0.285 Chirality : 0.044 0.145 499 Planarity : 0.004 0.039 584 Dihedral : 4.510 18.354 517 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.01 % Allowed : 17.24 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.34 (0.42), residues: 405 helix: -3.97 (0.66), residues: 27 sheet: -0.24 (0.44), residues: 148 loop : -0.89 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.008 0.001 TYR H 103 PHE 0.004 0.001 PHE R 456 TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 3350) covalent geometry : angle 0.53394 ( 4556) SS BOND : bond 0.00545 ( 6) SS BOND : angle 1.50318 ( 12) hydrogen bonds : bond 0.02879 ( 81) hydrogen bonds : angle 5.17099 ( 201) link_BETA1-4 : bond 0.00362 ( 2) link_BETA1-4 : angle 1.43329 ( 6) link_NAG-ASN : bond 0.00282 ( 1) link_NAG-ASN : angle 3.05939 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.121 Fit side-chains REVERT: L 48 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8363 (mp) REVERT: H 23 LYS cc_start: 0.8491 (tttp) cc_final: 0.8229 (tttm) REVERT: H 82 GLN cc_start: 0.7690 (mm110) cc_final: 0.7461 (mm110) REVERT: H 101 ASP cc_start: 0.8251 (t70) cc_final: 0.8027 (t70) outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.0684 time to fit residues: 6.2250 Evaluate side-chains 78 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.0170 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.106027 restraints weight = 4804.084| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.21 r_work: 0.3042 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3359 Z= 0.129 Angle : 0.539 5.832 4577 Z= 0.281 Chirality : 0.043 0.147 499 Planarity : 0.004 0.040 584 Dihedral : 4.453 19.180 517 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.01 % Allowed : 17.24 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.31 (0.42), residues: 405 helix: -3.97 (0.66), residues: 27 sheet: -0.22 (0.44), residues: 148 loop : -0.87 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.019 0.001 TYR H 27 PHE 0.004 0.001 PHE R 456 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3350) covalent geometry : angle 0.52702 ( 4556) SS BOND : bond 0.00549 ( 6) SS BOND : angle 1.46773 ( 12) hydrogen bonds : bond 0.02789 ( 81) hydrogen bonds : angle 5.12397 ( 201) link_BETA1-4 : bond 0.00326 ( 2) link_BETA1-4 : angle 1.39187 ( 6) link_NAG-ASN : bond 0.00225 ( 1) link_NAG-ASN : angle 3.09291 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1134.31 seconds wall clock time: 20 minutes 3.06 seconds (1203.06 seconds total)