Starting phenix.real_space_refine on Tue Mar 3 10:49:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzu_22574/03_2026/7jzu_22574.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzu_22574/03_2026/7jzu_22574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jzu_22574/03_2026/7jzu_22574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzu_22574/03_2026/7jzu_22574.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jzu_22574/03_2026/7jzu_22574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzu_22574/03_2026/7jzu_22574.map" } resolution = 3.1 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= 0.031 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 11 5.16 5 C 1270 2.51 5 N 325 2.21 5 O 381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 1987 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1512 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 182} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.60, per 1000 atoms: 0.30 Number of scatterers: 1987 At special positions: 0 Unit cell: (59.85, 71.4, 66.15, 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 11 16.00 O 381 8.00 N 325 7.00 C 1270 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=2.09 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.16 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 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: 0.19 Conformation dependent library (CDL) restraints added in 66.2 milliseconds 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 462 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 36.7% alpha, 16.1% 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 2 through 19 removed outlier: 3.566A pdb=" N LEU A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.781A pdb=" N LEU A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 removed outlier: 4.251A pdb=" N GLU A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.716A 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 390 removed outlier: 4.979A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.459A 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: 3.944A 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: 6.591A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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 80 hydrogen bonds defined for protein. 204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.15 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 571 1.33 - 1.46: 603 1.46 - 1.59: 846 1.59 - 1.73: 0 1.73 - 1.86: 14 Bond restraints: 2034 Sorted by residual: bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" CB ASN B 487 " pdb=" CG ASN B 487 " ideal model delta sigma weight residual 1.516 1.442 0.074 2.50e-02 1.60e+03 8.85e+00 bond pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 1.516 1.445 0.071 2.50e-02 1.60e+03 8.03e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.469 -0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" C5 FUC C 3 " pdb=" O5 FUC C 3 " ideal model delta sigma weight residual 1.423 1.476 -0.053 2.00e-02 2.50e+03 7.13e+00 ... (remaining 2029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 2134 1.42 - 2.85: 499 2.85 - 4.27: 87 4.27 - 5.70: 31 5.70 - 7.12: 9 Bond angle restraints: 2760 Sorted by residual: angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.56 126.07 -6.51 1.02e+00 9.61e-01 4.08e+01 angle pdb=" C PHE B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 119.56 125.95 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C LEU B 425 " pdb=" N PRO B 426 " pdb=" CA PRO B 426 " ideal model delta sigma weight residual 120.03 126.20 -6.17 9.90e-01 1.02e+00 3.89e+01 angle pdb=" C THR B 478 " pdb=" N PRO B 479 " pdb=" CA PRO B 479 " ideal model delta sigma weight residual 119.78 126.05 -6.27 1.03e+00 9.43e-01 3.71e+01 angle pdb=" C ALA B 411 " pdb=" N PRO B 412 " pdb=" CA PRO B 412 " ideal model delta sigma weight residual 119.76 125.81 -6.05 1.03e+00 9.43e-01 3.45e+01 ... (remaining 2755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.82: 1169 13.82 - 27.64: 52 27.64 - 41.46: 17 41.46 - 55.27: 4 55.27 - 69.09: 2 Dihedral angle restraints: 1244 sinusoidal: 519 harmonic: 725 Sorted by residual: dihedral pdb=" C TYR B 495 " pdb=" N TYR B 495 " pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " ideal model delta harmonic sigma weight residual -122.60 -114.96 -7.64 0 2.50e+00 1.60e-01 9.34e+00 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 93.00 116.81 -23.81 1 1.00e+01 1.00e-02 8.17e+00 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 69.09 -69.09 1 3.00e+01 1.11e-03 6.86e+00 ... (remaining 1241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 199 0.074 - 0.149: 81 0.149 - 0.223: 18 0.223 - 0.298: 4 0.298 - 0.372: 2 Chirality restraints: 304 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 -2.58 0.18 2.00e-02 2.50e+03 7.72e+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 -2.47 0.07 2.00e-02 2.50e+03 1.21e+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 -2.86 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 301 not shown) Planarity restraints: 356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.043 2.00e-02 2.50e+03 2.19e-02 9.57e+00 pdb=" CG TYR B 495 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.018 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 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 449 " 0.025 2.00e-02 2.50e+03 1.47e-02 4.34e+00 pdb=" CG TYR B 449 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 449 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 449 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 449 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B 449 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 449 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 449 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 505 " -0.026 2.00e-02 2.50e+03 1.45e-02 4.23e+00 pdb=" CG TYR B 505 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 505 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 505 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 505 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 505 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 505 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 505 " -0.023 2.00e-02 2.50e+03 ... (remaining 353 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1044 2.99 - 3.47: 1816 3.47 - 3.94: 3369 3.94 - 4.42: 3931 4.42 - 4.90: 6085 Nonbonded interactions: 16245 Sorted by model distance: nonbonded pdb=" N ALA B 520 " pdb=" O ALA B 520 " model vdw 2.509 2.496 nonbonded pdb=" N ASP B 428 " pdb=" OD1 ASP B 428 " model vdw 2.573 3.120 nonbonded pdb=" N ASN B 440 " pdb=" OD1 ASN B 440 " model vdw 2.586 3.120 nonbonded pdb=" N LYS B 462 " pdb=" O LYS B 462 " model vdw 2.597 2.496 nonbonded pdb=" N GLN B 506 " pdb=" O GLN B 506 " model vdw 2.617 2.496 ... (remaining 16240 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: 3.440 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: 2.970 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 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 : 0.015 0.126 2041 Z= 0.818 Angle : 1.357 7.124 2777 Z= 0.905 Chirality : 0.085 0.372 304 Planarity : 0.005 0.022 355 Dihedral : 9.379 69.093 770 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.23 (0.52), residues: 244 helix: -1.00 (0.53), residues: 78 sheet: 0.98 (0.75), residues: 49 loop : 0.87 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.043 0.006 TYR B 495 PHE 0.014 0.003 PHE B 497 TRP 0.020 0.006 TRP B 353 HIS 0.002 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.01477 ( 2034) covalent geometry : angle 1.34354 ( 2760) SS BOND : bond 0.07104 ( 4) SS BOND : angle 2.48932 ( 8) hydrogen bonds : bond 0.18316 ( 80) hydrogen bonds : angle 8.72729 ( 204) link_BETA1-4 : bond 0.07263 ( 1) link_BETA1-4 : angle 3.79002 ( 3) link_BETA1-6 : bond 0.05027 ( 1) link_BETA1-6 : angle 2.19551 ( 3) link_NAG-ASN : bond 0.05641 ( 1) link_NAG-ASN : angle 2.67644 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.047 Fit side-chains REVERT: B 361 CYS cc_start: 0.6296 (p) cc_final: 0.5722 (p) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0607 time to fit residues: 3.3801 Evaluate side-chains 32 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 0.0870 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 9 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.0050 chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 overall best weight: 0.1572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 487 ASN B 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.159072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.145975 restraints weight = 2302.976| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.15 r_work: 0.3527 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2041 Z= 0.146 Angle : 0.574 6.420 2777 Z= 0.296 Chirality : 0.044 0.165 304 Planarity : 0.004 0.041 355 Dihedral : 4.241 15.159 334 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 4.41 % Favored : 93.63 % 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: 0.62 (0.54), residues: 244 helix: 0.16 (0.62), residues: 73 sheet: 0.60 (0.79), residues: 48 loop : 0.71 (0.56), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.023 0.002 TYR B 495 PHE 0.012 0.001 PHE B 497 TRP 0.006 0.001 TRP B 436 HIS 0.005 0.003 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 2034) covalent geometry : angle 0.56654 ( 2760) SS BOND : bond 0.00076 ( 4) SS BOND : angle 0.46417 ( 8) hydrogen bonds : bond 0.04908 ( 80) hydrogen bonds : angle 6.22420 ( 204) link_BETA1-4 : bond 0.00158 ( 1) link_BETA1-4 : angle 1.88863 ( 3) link_BETA1-6 : bond 0.00032 ( 1) link_BETA1-6 : angle 1.65052 ( 3) link_NAG-ASN : bond 0.00256 ( 1) link_NAG-ASN : angle 1.82460 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.074 Fit side-chains REVERT: A 13 MET cc_start: 0.8460 (ptm) cc_final: 0.8038 (ptt) REVERT: A 29 SER cc_start: 0.8221 (t) cc_final: 0.7777 (p) REVERT: B 361 CYS cc_start: 0.7379 (p) cc_final: 0.6736 (p) outliers start: 4 outliers final: 2 residues processed: 46 average time/residue: 0.0613 time to fit residues: 3.3334 Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 0 optimal weight: 0.3980 chunk 13 optimal weight: 0.0030 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 overall best weight: 0.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS B 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.156025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143630 restraints weight = 2321.007| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.11 r_work: 0.3536 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2041 Z= 0.164 Angle : 0.550 4.327 2777 Z= 0.287 Chirality : 0.044 0.129 304 Planarity : 0.004 0.052 355 Dihedral : 4.157 15.941 334 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.45 % Allowed : 6.37 % Favored : 91.18 % 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: 0.46 (0.55), residues: 244 helix: 0.35 (0.62), residues: 81 sheet: 0.21 (0.75), residues: 48 loop : 0.54 (0.59), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.024 0.002 TYR B 495 PHE 0.009 0.001 PHE B 456 TRP 0.007 0.001 TRP B 436 HIS 0.004 0.002 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 2034) covalent geometry : angle 0.53876 ( 2760) SS BOND : bond 0.00392 ( 4) SS BOND : angle 0.79237 ( 8) hydrogen bonds : bond 0.04576 ( 80) hydrogen bonds : angle 5.88326 ( 204) link_BETA1-4 : bond 0.00305 ( 1) link_BETA1-4 : angle 2.14772 ( 3) link_BETA1-6 : bond 0.00044 ( 1) link_BETA1-6 : angle 1.48861 ( 3) link_NAG-ASN : bond 0.00214 ( 1) link_NAG-ASN : angle 2.03865 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.062 Fit side-chains REVERT: A 29 SER cc_start: 0.8273 (t) cc_final: 0.7775 (p) REVERT: B 361 CYS cc_start: 0.7528 (p) cc_final: 0.6921 (p) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.0708 time to fit residues: 3.4017 Evaluate side-chains 40 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.2980 chunk 0 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 chunk 15 optimal weight: 0.0970 chunk 19 optimal weight: 0.0970 chunk 22 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 overall best weight: 0.1174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.145476 restraints weight = 2325.114| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.12 r_work: 0.3543 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2041 Z= 0.110 Angle : 0.476 3.673 2777 Z= 0.249 Chirality : 0.043 0.127 304 Planarity : 0.004 0.050 355 Dihedral : 4.031 20.589 334 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.98 % Allowed : 8.82 % Favored : 90.20 % 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: 0.83 (0.55), residues: 244 helix: 1.00 (0.64), residues: 73 sheet: 0.15 (0.75), residues: 48 loop : 0.63 (0.58), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.016 0.001 TYR B 495 PHE 0.005 0.001 PHE B 456 TRP 0.008 0.001 TRP B 436 HIS 0.000 0.000 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 2034) covalent geometry : angle 0.46749 ( 2760) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.78551 ( 8) hydrogen bonds : bond 0.03665 ( 80) hydrogen bonds : angle 5.54162 ( 204) link_BETA1-4 : bond 0.00287 ( 1) link_BETA1-4 : angle 1.71177 ( 3) link_BETA1-6 : bond 0.00112 ( 1) link_BETA1-6 : angle 1.30546 ( 3) link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 1.62739 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.076 Fit side-chains REVERT: A 29 SER cc_start: 0.8344 (t) cc_final: 0.7812 (p) REVERT: B 361 CYS cc_start: 0.7517 (p) cc_final: 0.6923 (p) outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.0643 time to fit residues: 3.0195 Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 6 optimal weight: 0.0870 chunk 12 optimal weight: 0.2980 chunk 21 optimal weight: 0.0970 chunk 15 optimal weight: 0.0370 chunk 11 optimal weight: 0.1980 overall best weight: 0.1234 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.162205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.151753 restraints weight = 2282.613| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 0.81 r_work: 0.3613 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2041 Z= 0.108 Angle : 0.488 6.980 2777 Z= 0.248 Chirality : 0.042 0.122 304 Planarity : 0.004 0.051 355 Dihedral : 3.976 21.307 334 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.47 % Allowed : 9.80 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.56), residues: 244 helix: 1.28 (0.65), residues: 73 sheet: -0.01 (0.76), residues: 50 loop : 0.65 (0.59), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 457 TYR 0.016 0.001 TYR B 495 PHE 0.005 0.001 PHE B 456 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 2034) covalent geometry : angle 0.47750 ( 2760) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.95052 ( 8) hydrogen bonds : bond 0.03479 ( 80) hydrogen bonds : angle 5.53573 ( 204) link_BETA1-4 : bond 0.00285 ( 1) link_BETA1-4 : angle 1.87497 ( 3) link_BETA1-6 : bond 0.00147 ( 1) link_BETA1-6 : angle 1.27445 ( 3) link_NAG-ASN : bond 0.00127 ( 1) link_NAG-ASN : angle 1.69932 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.072 Fit side-chains REVERT: A 29 SER cc_start: 0.8309 (t) cc_final: 0.7858 (p) REVERT: B 361 CYS cc_start: 0.7190 (p) cc_final: 0.6561 (p) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.0620 time to fit residues: 2.8289 Evaluate side-chains 40 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 0.0870 chunk 0 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.0670 chunk 6 optimal weight: 0.0970 chunk 9 optimal weight: 0.0010 chunk 4 optimal weight: 0.4980 chunk 23 optimal weight: 0.3980 chunk 12 optimal weight: 0.0870 chunk 7 optimal weight: 0.5980 overall best weight: 0.0678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.163528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.153422 restraints weight = 2279.890| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 0.78 r_work: 0.3633 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2041 Z= 0.084 Angle : 0.447 6.832 2777 Z= 0.226 Chirality : 0.042 0.123 304 Planarity : 0.004 0.050 355 Dihedral : 3.904 24.454 334 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.96 % Allowed : 10.29 % Favored : 87.75 % 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: 1.17 (0.56), residues: 244 helix: 1.91 (0.69), residues: 67 sheet: -0.05 (0.77), residues: 49 loop : 0.66 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 408 TYR 0.012 0.001 TYR B 495 PHE 0.004 0.001 PHE B 377 TRP 0.008 0.001 TRP B 436 HIS 0.000 0.000 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 2034) covalent geometry : angle 0.44006 ( 2760) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.74315 ( 8) hydrogen bonds : bond 0.03012 ( 80) hydrogen bonds : angle 5.40028 ( 204) link_BETA1-4 : bond 0.00318 ( 1) link_BETA1-4 : angle 1.49860 ( 3) link_BETA1-6 : bond 0.00261 ( 1) link_BETA1-6 : angle 1.23300 ( 3) link_NAG-ASN : bond 0.00003 ( 1) link_NAG-ASN : angle 1.33823 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.079 Fit side-chains REVERT: A 29 SER cc_start: 0.8216 (t) cc_final: 0.7829 (p) REVERT: B 361 CYS cc_start: 0.7155 (p) cc_final: 0.6554 (p) outliers start: 4 outliers final: 4 residues processed: 42 average time/residue: 0.0619 time to fit residues: 3.0800 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 9 optimal weight: 0.0670 chunk 12 optimal weight: 0.0980 chunk 15 optimal weight: 0.0040 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 21 optimal weight: 0.3980 chunk 22 optimal weight: 0.2980 chunk 11 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 overall best weight: 0.0888 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.161792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.151555 restraints weight = 2299.522| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 0.83 r_work: 0.3607 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2041 Z= 0.101 Angle : 0.504 7.981 2777 Z= 0.252 Chirality : 0.043 0.131 304 Planarity : 0.004 0.048 355 Dihedral : 4.091 23.896 334 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.96 % Allowed : 9.80 % Favored : 88.24 % 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: 1.20 (0.56), residues: 244 helix: 1.96 (0.69), residues: 67 sheet: -0.09 (0.76), residues: 49 loop : 0.68 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 403 TYR 0.013 0.001 TYR B 495 PHE 0.006 0.001 PHE B 392 TRP 0.007 0.001 TRP B 436 HIS 0.000 0.000 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 2034) covalent geometry : angle 0.48852 ( 2760) SS BOND : bond 0.00548 ( 4) SS BOND : angle 1.86830 ( 8) hydrogen bonds : bond 0.03086 ( 80) hydrogen bonds : angle 5.41923 ( 204) link_BETA1-4 : bond 0.00208 ( 1) link_BETA1-4 : angle 1.64293 ( 3) link_BETA1-6 : bond 0.00248 ( 1) link_BETA1-6 : angle 1.23019 ( 3) link_NAG-ASN : bond 0.00049 ( 1) link_NAG-ASN : angle 1.51019 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.081 Fit side-chains REVERT: A 17 ASP cc_start: 0.7037 (m-30) cc_final: 0.6624 (m-30) REVERT: A 29 SER cc_start: 0.8172 (t) cc_final: 0.7824 (p) REVERT: B 361 CYS cc_start: 0.7138 (p) cc_final: 0.6530 (p) outliers start: 4 outliers final: 4 residues processed: 40 average time/residue: 0.0556 time to fit residues: 2.6823 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 0.0770 chunk 22 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 20 optimal weight: 0.1980 overall best weight: 0.1916 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.162376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146086 restraints weight = 2315.069| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.64 r_work: 0.3600 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2041 Z= 0.141 Angle : 0.537 8.126 2777 Z= 0.268 Chirality : 0.044 0.129 304 Planarity : 0.004 0.049 355 Dihedral : 4.202 21.407 334 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.94 % Allowed : 9.31 % Favored : 87.75 % 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: 0.96 (0.56), residues: 244 helix: 1.97 (0.69), residues: 67 sheet: -0.12 (0.76), residues: 49 loop : 0.36 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.019 0.002 TYR B 495 PHE 0.009 0.001 PHE B 456 TRP 0.006 0.001 TRP B 436 HIS 0.001 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2034) covalent geometry : angle 0.51938 ( 2760) SS BOND : bond 0.00186 ( 4) SS BOND : angle 1.62452 ( 8) hydrogen bonds : bond 0.03528 ( 80) hydrogen bonds : angle 5.62243 ( 204) link_BETA1-4 : bond 0.00271 ( 1) link_BETA1-4 : angle 2.28133 ( 3) link_BETA1-6 : bond 0.00148 ( 1) link_BETA1-6 : angle 1.22626 ( 3) link_NAG-ASN : bond 0.00284 ( 1) link_NAG-ASN : angle 2.23276 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7050 (m-30) cc_final: 0.6544 (m-30) REVERT: A 29 SER cc_start: 0.8299 (t) cc_final: 0.7846 (p) REVERT: B 457 ARG cc_start: 0.8723 (ttt90) cc_final: 0.8516 (ttt90) outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 0.0539 time to fit residues: 2.6460 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 0.0980 chunk 11 optimal weight: 0.0980 chunk 20 optimal weight: 0.0970 chunk 18 optimal weight: 0.0980 chunk 7 optimal weight: 0.3980 chunk 12 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.0020 chunk 1 optimal weight: 0.0770 chunk 13 optimal weight: 0.0770 chunk 10 optimal weight: 0.1980 overall best weight: 0.0700 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.168620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.152416 restraints weight = 2263.819| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.62 r_work: 0.3640 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2041 Z= 0.091 Angle : 0.498 8.516 2777 Z= 0.248 Chirality : 0.042 0.122 304 Planarity : 0.004 0.047 355 Dihedral : 4.151 25.830 334 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.47 % Allowed : 11.27 % Favored : 87.25 % 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: 0.97 (0.56), residues: 244 helix: 2.03 (0.69), residues: 67 sheet: -0.17 (0.75), residues: 49 loop : 0.35 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.011 0.001 TYR B 495 PHE 0.004 0.001 PHE B 456 TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 2034) covalent geometry : angle 0.48738 ( 2760) SS BOND : bond 0.00307 ( 4) SS BOND : angle 1.27757 ( 8) hydrogen bonds : bond 0.03078 ( 80) hydrogen bonds : angle 5.52548 ( 204) link_BETA1-4 : bond 0.00293 ( 1) link_BETA1-4 : angle 1.75516 ( 3) link_BETA1-6 : bond 0.00240 ( 1) link_BETA1-6 : angle 1.22545 ( 3) link_NAG-ASN : bond 0.00011 ( 1) link_NAG-ASN : angle 1.58343 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7596 (ttp) REVERT: A 17 ASP cc_start: 0.7005 (m-30) cc_final: 0.6490 (m-30) REVERT: A 29 SER cc_start: 0.8203 (t) cc_final: 0.7728 (p) REVERT: A 38 LYS cc_start: 0.5975 (mmmt) cc_final: 0.4643 (tptp) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.0437 time to fit residues: 2.0531 Evaluate side-chains 41 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 8 optimal weight: 0.0050 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 10 optimal weight: 0.2980 chunk 5 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 overall best weight: 0.1392 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.167132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.150754 restraints weight = 2290.598| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.64 r_work: 0.3618 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2041 Z= 0.115 Angle : 0.521 8.605 2777 Z= 0.258 Chirality : 0.043 0.120 304 Planarity : 0.004 0.046 355 Dihedral : 4.169 24.363 334 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.47 % Allowed : 10.78 % Favored : 87.75 % 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: 1.07 (0.56), residues: 244 helix: 2.11 (0.69), residues: 67 sheet: 0.19 (0.85), residues: 39 loop : 0.26 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.017 0.001 TYR B 495 PHE 0.006 0.001 PHE B 456 TRP 0.006 0.001 TRP B 436 HIS 0.001 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2034) covalent geometry : angle 0.50618 ( 2760) SS BOND : bond 0.00331 ( 4) SS BOND : angle 1.49199 ( 8) hydrogen bonds : bond 0.03256 ( 80) hydrogen bonds : angle 5.56701 ( 204) link_BETA1-4 : bond 0.00267 ( 1) link_BETA1-4 : angle 2.07920 ( 3) link_BETA1-6 : bond 0.00243 ( 1) link_BETA1-6 : angle 1.14154 ( 3) link_NAG-ASN : bond 0.00182 ( 1) link_NAG-ASN : angle 1.95551 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7688 (ttp) REVERT: A 17 ASP cc_start: 0.7083 (m-30) cc_final: 0.6583 (m-30) REVERT: A 29 SER cc_start: 0.8251 (t) cc_final: 0.7767 (p) REVERT: A 38 LYS cc_start: 0.6021 (mmmt) cc_final: 0.4678 (tptp) REVERT: B 457 ARG cc_start: 0.8715 (ttt90) cc_final: 0.8436 (ttm-80) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.0590 time to fit residues: 2.6890 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 5 optimal weight: 0.0870 chunk 14 optimal weight: 0.3980 chunk 11 optimal weight: 0.0770 chunk 16 optimal weight: 0.1980 chunk 9 optimal weight: 0.0970 chunk 21 optimal weight: 0.0470 chunk 8 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 overall best weight: 0.0810 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.169111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.153015 restraints weight = 2300.109| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.62 r_work: 0.3627 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2041 Z= 0.089 Angle : 0.481 8.106 2777 Z= 0.239 Chirality : 0.042 0.123 304 Planarity : 0.004 0.046 355 Dihedral : 4.158 28.036 334 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.47 % Allowed : 10.78 % Favored : 87.75 % 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: 1.08 (0.56), residues: 244 helix: 2.09 (0.69), residues: 68 sheet: 0.18 (0.85), residues: 39 loop : 0.26 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 408 TYR 0.011 0.001 TYR B 495 PHE 0.004 0.001 PHE B 377 TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 2034) covalent geometry : angle 0.47070 ( 2760) SS BOND : bond 0.00180 ( 4) SS BOND : angle 1.21276 ( 8) hydrogen bonds : bond 0.02935 ( 80) hydrogen bonds : angle 5.45185 ( 204) link_BETA1-4 : bond 0.00338 ( 1) link_BETA1-4 : angle 1.61851 ( 3) link_BETA1-6 : bond 0.00245 ( 1) link_BETA1-6 : angle 1.20966 ( 3) link_NAG-ASN : bond 0.00008 ( 1) link_NAG-ASN : angle 1.46533 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 961.01 seconds wall clock time: 17 minutes 21.73 seconds (1041.73 seconds total)