Starting phenix.real_space_refine on Wed Jul 1 22:25:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wm0_32596/07_2026/7wm0_32596.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wm0_32596/07_2026/7wm0_32596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wm0_32596/07_2026/7wm0_32596.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wm0_32596/07_2026/7wm0_32596.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wm0_32596/07_2026/7wm0_32596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wm0_32596/07_2026/7wm0_32596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wm0_32596/07_2026/7wm0_32596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wm0_32596/07_2026/7wm0_32596.map" } resolution = 3.35 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= 0.005 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 17 5.16 5 C 2146 2.51 5 N 573 2.21 5 O 640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3376 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1554 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Chain: "L" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.02, per 1000 atoms: 0.30 Number of scatterers: 3376 At special positions: 0 Unit cell: (71.994, 79.092, 70.98, 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 17 16.00 O 640 8.00 N 573 7.00 C 2146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.01 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 122.0 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 10.4% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.113A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.814A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.373A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.373A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.805A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.664A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.561A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 243 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: 0.46 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1016 1.34 - 1.46: 795 1.46 - 1.59: 1630 1.59 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 3463 Sorted by residual: bond pdb=" N ILE B 472 " pdb=" CA ILE B 472 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" N VAL L 88 " pdb=" CA VAL L 88 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.14e-02 7.69e+03 1.18e+01 bond pdb=" N LYS B 444 " pdb=" CA LYS B 444 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N ILE B 402 " pdb=" CA ILE B 402 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" N ASN H 54 " pdb=" CA ASN H 54 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.10e-02 8.26e+03 9.66e+00 ... (remaining 3458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 3960 1.62 - 3.23: 630 3.23 - 4.85: 96 4.85 - 6.47: 15 6.47 - 8.09: 6 Bond angle restraints: 4707 Sorted by residual: angle pdb=" N SER B 366 " pdb=" CA SER B 366 " pdb=" C SER B 366 " ideal model delta sigma weight residual 111.71 105.91 5.80 1.15e+00 7.56e-01 2.54e+01 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 109.85 116.70 -6.85 1.58e+00 4.01e-01 1.88e+01 angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 112.90 108.75 4.15 9.60e-01 1.09e+00 1.87e+01 angle pdb=" C VAL B 407 " pdb=" N ARG B 408 " pdb=" CA ARG B 408 " ideal model delta sigma weight residual 120.38 126.29 -5.91 1.37e+00 5.33e-01 1.86e+01 angle pdb=" N TYR B 369 " pdb=" CA TYR B 369 " pdb=" C TYR B 369 " ideal model delta sigma weight residual 112.89 108.02 4.87 1.24e+00 6.50e-01 1.54e+01 ... (remaining 4702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 1788 13.97 - 27.95: 173 27.95 - 41.92: 51 41.92 - 55.90: 11 55.90 - 69.87: 7 Dihedral angle restraints: 2030 sinusoidal: 789 harmonic: 1241 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 126.08 -33.08 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" C ARG B 466 " pdb=" N ARG B 466 " pdb=" CA ARG B 466 " pdb=" CB ARG B 466 " ideal model delta harmonic sigma weight residual -122.60 -114.01 -8.59 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" C TYR B 365 " pdb=" N TYR B 365 " pdb=" CA TYR B 365 " pdb=" CB TYR B 365 " ideal model delta harmonic sigma weight residual -122.60 -114.17 -8.43 0 2.50e+00 1.60e-01 1.14e+01 ... (remaining 2027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 340 0.067 - 0.133: 117 0.133 - 0.200: 39 0.200 - 0.267: 8 0.267 - 0.333: 2 Chirality restraints: 506 Sorted by residual: chirality pdb=" CA ILE L 2 " pdb=" N ILE L 2 " pdb=" C ILE L 2 " pdb=" CB ILE L 2 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ARG B 466 " pdb=" N ARG B 466 " pdb=" C ARG B 466 " pdb=" CB ARG B 466 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA TYR H 115 " pdb=" N TYR H 115 " pdb=" C TYR H 115 " pdb=" CB TYR H 115 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 503 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.355 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG B1301 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.137 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 353 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C TRP B 353 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP B 353 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 354 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 116 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C GLY H 116 " 0.037 2.00e-02 2.50e+03 pdb=" O GLY H 116 " -0.014 2.00e-02 2.50e+03 pdb=" N MET H 117 " -0.013 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.90: 1446 2.90 - 3.40: 3021 3.40 - 3.90: 5401 3.90 - 4.40: 6057 4.40 - 4.90: 10403 Nonbonded interactions: 26328 Sorted by model distance: nonbonded pdb=" OD1 ASP H 62 " pdb=" N SER H 63 " model vdw 2.405 3.120 nonbonded pdb=" OD1 ASP H 118 " pdb=" N VAL H 119 " model vdw 2.423 3.120 nonbonded pdb=" NH1 ARG L 59 " pdb=" O PHE L 67 " model vdw 2.452 3.120 nonbonded pdb=" O SER H 130 " pdb=" OG SER H 130 " model vdw 2.456 3.040 nonbonded pdb=" NE2 GLN L 95 " pdb=" O PRO L 100 " model vdw 2.457 3.120 ... (remaining 26323 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: 3.800 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5553 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.044 3470 Z= 0.653 Angle : 1.227 8.086 4722 Z= 0.851 Chirality : 0.078 0.333 506 Planarity : 0.013 0.304 611 Dihedral : 12.609 69.871 1226 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.28 % Allowed : 6.89 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -2.87 (0.38), residues: 424 helix: -4.69 (0.22), residues: 39 sheet: -1.16 (0.45), residues: 142 loop : -1.89 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 454 TYR 0.012 0.002 TYR B 396 PHE 0.012 0.002 PHE B 515 TRP 0.008 0.002 TRP B 353 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00911 / 0.65 ( 3463) covalent geometry : angle 1.22259 / 0.85 ( 4707) SS BOND : bond 0.00851 / 0.43 ( 6) SS BOND : angle 2.24132 / 1.41 ( 12) hydrogen bonds : bond 0.20976 / 12.75 ( 102) hydrogen bonds : angle 9.12852 / 6.44 ( 243) link_NAG-ASN : bond 0.00929 / 0.49 ( 1) link_NAG-ASN : angle 1.90602 / 0.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ASP cc_start: 0.8174 (m-30) cc_final: 0.7972 (m-30) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.0678 time to fit residues: 7.1009 Evaluate side-chains 55 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN H 13 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.167128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.151009 restraints weight = 7770.480| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 4.38 r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 3470 Z= 0.210 Angle : 0.735 8.094 4722 Z= 0.382 Chirality : 0.047 0.168 506 Planarity : 0.005 0.036 611 Dihedral : 5.037 21.247 478 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.48 % Allowed : 11.57 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.83 (0.39), residues: 424 helix: -4.58 (0.44), residues: 20 sheet: -0.69 (0.47), residues: 130 loop : -1.23 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 59 TYR 0.015 0.002 TYR L 92 PHE 0.024 0.002 PHE B 464 TRP 0.015 0.003 TRP B 436 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 3463) covalent geometry : angle 0.72372 / 0.38 ( 4707) SS BOND : bond 0.00421 / 0.24 ( 6) SS BOND : angle 1.56669 / 0.88 ( 12) hydrogen bonds : bond 0.04001 / 2.60 ( 102) hydrogen bonds : angle 6.87412 / 4.74 ( 243) link_NAG-ASN : bond 0.00508 / 0.27 ( 1) link_NAG-ASN : angle 4.31718 / 2.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.125 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.0621 time to fit residues: 5.6241 Evaluate side-chains 61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN L 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.169836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.157572 restraints weight = 7503.437| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 3.56 r_work: 0.4259 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3470 Z= 0.190 Angle : 0.696 7.162 4722 Z= 0.361 Chirality : 0.046 0.248 506 Planarity : 0.005 0.036 611 Dihedral : 5.288 22.730 478 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.68 % Allowed : 15.70 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.58 (0.39), residues: 424 helix: -4.75 (0.46), residues: 26 sheet: -0.25 (0.47), residues: 130 loop : -1.07 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 408 TYR 0.021 0.002 TYR B 508 PHE 0.012 0.002 PHE L 67 TRP 0.024 0.002 TRP B 436 HIS 0.007 0.002 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 3463) covalent geometry : angle 0.69051 / 0.36 ( 4707) SS BOND : bond 0.00674 / 0.36 ( 6) SS BOND : angle 1.39598 / 0.80 ( 12) hydrogen bonds : bond 0.04418 / 2.71 ( 102) hydrogen bonds : angle 6.49039 / 4.56 ( 243) link_NAG-ASN : bond 0.00251 / 0.13 ( 1) link_NAG-ASN : angle 2.34135 / 1.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 378 LYS cc_start: 0.7490 (mtmt) cc_final: 0.7163 (mmtm) REVERT: B 405 ASP cc_start: 0.5992 (m-30) cc_final: 0.5730 (t0) REVERT: L 87 ASP cc_start: 0.4340 (OUTLIER) cc_final: 0.3379 (t70) outliers start: 17 outliers final: 12 residues processed: 71 average time/residue: 0.0570 time to fit residues: 5.1759 Evaluate side-chains 63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.0470 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 460 ASN H 74 ASN L 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.165690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.153575 restraints weight = 7324.054| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 3.44 r_work: 0.4258 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3470 Z= 0.190 Angle : 0.712 8.011 4722 Z= 0.364 Chirality : 0.046 0.230 506 Planarity : 0.005 0.035 611 Dihedral : 5.359 23.836 478 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.79 % Allowed : 17.63 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.36 (0.40), residues: 424 helix: -4.84 (0.37), residues: 26 sheet: 0.15 (0.48), residues: 131 loop : -1.05 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 403 TYR 0.044 0.002 TYR B 508 PHE 0.011 0.002 PHE H 29 TRP 0.023 0.002 TRP B 436 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 3463) covalent geometry : angle 0.70803 / 0.36 ( 4707) SS BOND : bond 0.00453 / 0.25 ( 6) SS BOND : angle 1.00007 / 0.57 ( 12) hydrogen bonds : bond 0.04057 / 2.53 ( 102) hydrogen bonds : angle 6.59832 / 4.63 ( 243) link_NAG-ASN : bond 0.00098 / 0.05 ( 1) link_NAG-ASN : angle 2.60578 / 1.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: B 378 LYS cc_start: 0.7437 (mtmt) cc_final: 0.7235 (mmtm) REVERT: B 449 TYR cc_start: 0.6795 (t80) cc_final: 0.6409 (t80) REVERT: L 47 GLN cc_start: 0.5542 (mp10) cc_final: 0.5333 (mp10) outliers start: 21 outliers final: 15 residues processed: 82 average time/residue: 0.0688 time to fit residues: 6.8906 Evaluate side-chains 65 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.0270 chunk 17 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 13 GLN H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.162321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.150743 restraints weight = 7412.600| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 3.36 r_work: 0.4189 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.6923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3470 Z= 0.215 Angle : 0.751 7.791 4722 Z= 0.384 Chirality : 0.047 0.282 506 Planarity : 0.005 0.037 611 Dihedral : 5.708 25.867 478 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.23 % Allowed : 22.04 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.44 (0.40), residues: 424 helix: -5.00 (0.25), residues: 26 sheet: 0.20 (0.49), residues: 129 loop : -1.15 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 403 TYR 0.045 0.003 TYR B 508 PHE 0.011 0.002 PHE B 375 TRP 0.030 0.003 TRP B 436 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 ( 3463) covalent geometry : angle 0.74760 / 0.38 ( 4707) SS BOND : bond 0.00446 / 0.26 ( 6) SS BOND : angle 1.10716 / 0.64 ( 12) hydrogen bonds : bond 0.04103 / 2.49 ( 102) hydrogen bonds : angle 6.59504 / 4.59 ( 243) link_NAG-ASN : bond 0.00058 / 0.03 ( 1) link_NAG-ASN : angle 2.59526 / 1.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: H 98 LYS cc_start: 0.8344 (ttpp) cc_final: 0.8051 (pttm) REVERT: L 47 GLN cc_start: 0.5960 (mp10) cc_final: 0.5650 (mp10) outliers start: 19 outliers final: 16 residues processed: 79 average time/residue: 0.0649 time to fit residues: 6.3825 Evaluate side-chains 73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 27 GLN ** 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 = 0.4512 r_free = 0.4512 target = 0.162780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.151323 restraints weight = 7570.409| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 3.50 r_work: 0.4200 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.7371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3470 Z= 0.183 Angle : 0.711 8.954 4722 Z= 0.365 Chirality : 0.047 0.260 506 Planarity : 0.005 0.037 611 Dihedral : 5.585 25.501 478 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.34 % Allowed : 22.59 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.40), residues: 424 helix: -5.02 (0.23), residues: 26 sheet: 0.24 (0.49), residues: 128 loop : -1.20 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 454 TYR 0.053 0.002 TYR B 508 PHE 0.017 0.002 PHE B 429 TRP 0.018 0.002 TRP B 436 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 3463) covalent geometry : angle 0.70802 / 0.36 ( 4707) SS BOND : bond 0.00486 / 0.27 ( 6) SS BOND : angle 0.97050 / 0.54 ( 12) hydrogen bonds : bond 0.03761 / 2.33 ( 102) hydrogen bonds : angle 6.48292 / 4.50 ( 243) link_NAG-ASN : bond 0.00008 / 0.00 ( 1) link_NAG-ASN : angle 2.55185 / 1.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: L 47 GLN cc_start: 0.6183 (mp10) cc_final: 0.5815 (mp10) REVERT: L 76 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6188 (m-80) outliers start: 23 outliers final: 20 residues processed: 79 average time/residue: 0.0517 time to fit residues: 5.3004 Evaluate side-chains 76 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.158591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.148089 restraints weight = 7299.904| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 3.19 r_work: 0.4095 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.7478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3470 Z= 0.130 Angle : 0.655 8.338 4722 Z= 0.333 Chirality : 0.045 0.242 506 Planarity : 0.004 0.032 611 Dihedral : 5.170 23.073 478 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.41 % Allowed : 26.17 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.37 (0.40), residues: 424 helix: -4.99 (0.24), residues: 26 sheet: 0.36 (0.52), residues: 118 loop : -1.10 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 454 TYR 0.038 0.002 TYR B 508 PHE 0.014 0.001 PHE B 429 TRP 0.014 0.002 TRP B 436 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 3463) covalent geometry : angle 0.65267 / 0.33 ( 4707) SS BOND : bond 0.00392 / 0.20 ( 6) SS BOND : angle 0.78148 / 0.45 ( 12) hydrogen bonds : bond 0.03295 / 2.08 ( 102) hydrogen bonds : angle 6.19098 / 4.29 ( 243) link_NAG-ASN : bond 0.00147 / 0.08 ( 1) link_NAG-ASN : angle 2.23621 / 1.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: L 47 GLN cc_start: 0.6132 (mp10) cc_final: 0.5803 (mp10) outliers start: 16 outliers final: 14 residues processed: 77 average time/residue: 0.0510 time to fit residues: 5.1408 Evaluate side-chains 70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 90 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0010 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.154768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.144135 restraints weight = 7332.083| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 3.17 r_work: 0.4049 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.7885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3470 Z= 0.199 Angle : 0.723 8.896 4722 Z= 0.370 Chirality : 0.048 0.281 506 Planarity : 0.005 0.036 611 Dihedral : 5.585 24.462 478 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.79 % Allowed : 25.90 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.51 (0.40), residues: 424 helix: -5.01 (0.22), residues: 26 sheet: 0.57 (0.53), residues: 113 loop : -1.35 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.025 0.002 TYR B 508 PHE 0.014 0.002 PHE B 374 TRP 0.023 0.002 TRP B 436 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 ( 3463) covalent geometry : angle 0.71967 / 0.37 ( 4707) SS BOND : bond 0.00477 / 0.26 ( 6) SS BOND : angle 1.10513 / 0.64 ( 12) hydrogen bonds : bond 0.03860 / 2.43 ( 102) hydrogen bonds : angle 6.45810 / 4.48 ( 243) link_NAG-ASN : bond 0.00023 / 0.01 ( 1) link_NAG-ASN : angle 2.49275 / 1.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 47 GLN cc_start: 0.6332 (mp10) cc_final: 0.5960 (mp10) REVERT: L 76 PHE cc_start: 0.6801 (OUTLIER) cc_final: 0.5896 (m-80) outliers start: 21 outliers final: 18 residues processed: 79 average time/residue: 0.0518 time to fit residues: 5.3176 Evaluate side-chains 79 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain L residue 90 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 0.4980 chunk 3 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.155814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.144831 restraints weight = 7223.598| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 3.22 r_work: 0.4065 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.8002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3470 Z= 0.166 Angle : 0.707 9.546 4722 Z= 0.358 Chirality : 0.047 0.271 506 Planarity : 0.004 0.036 611 Dihedral : 5.507 23.742 478 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.96 % Allowed : 26.72 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.57 (0.40), residues: 424 helix: -5.03 (0.21), residues: 26 sheet: 0.54 (0.53), residues: 113 loop : -1.40 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 454 TYR 0.022 0.002 TYR B 508 PHE 0.011 0.002 PHE B 374 TRP 0.018 0.002 TRP B 436 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 3463) covalent geometry : angle 0.70433 / 0.36 ( 4707) SS BOND : bond 0.00426 / 0.24 ( 6) SS BOND : angle 1.02306 / 0.59 ( 12) hydrogen bonds : bond 0.03643 / 2.29 ( 102) hydrogen bonds : angle 6.16940 / 4.27 ( 243) link_NAG-ASN : bond 0.00054 / 0.03 ( 1) link_NAG-ASN : angle 2.21724 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 47 GLN cc_start: 0.6377 (mp10) cc_final: 0.6068 (mp10) outliers start: 18 outliers final: 18 residues processed: 73 average time/residue: 0.0518 time to fit residues: 4.8847 Evaluate side-chains 73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 16 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 1 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.0030 overall best weight: 0.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.159499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.147820 restraints weight = 7165.446| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 3.32 r_work: 0.4112 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.8050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3470 Z= 0.121 Angle : 0.656 7.346 4722 Z= 0.332 Chirality : 0.045 0.243 506 Planarity : 0.004 0.039 611 Dihedral : 5.123 20.673 478 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.86 % Allowed : 28.65 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.54 (0.40), residues: 424 helix: -4.98 (0.22), residues: 26 sheet: 0.42 (0.53), residues: 113 loop : -1.30 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.014 0.001 TYR B 508 PHE 0.009 0.001 PHE B 429 TRP 0.009 0.001 TRP H 36 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 3463) covalent geometry : angle 0.65230 / 0.33 ( 4707) SS BOND : bond 0.00299 / 0.17 ( 6) SS BOND : angle 1.30551 / 0.75 ( 12) hydrogen bonds : bond 0.03365 / 2.13 ( 102) hydrogen bonds : angle 5.91222 / 4.06 ( 243) link_NAG-ASN : bond 0.00211 / 0.11 ( 1) link_NAG-ASN : angle 1.83739 / 0.99 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 47 GLN cc_start: 0.6168 (mp10) cc_final: 0.5892 (mp10) outliers start: 14 outliers final: 13 residues processed: 68 average time/residue: 0.0516 time to fit residues: 4.5652 Evaluate side-chains 69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.153209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.141273 restraints weight = 7580.564| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 3.66 r_work: 0.4011 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.8307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3470 Z= 0.209 Angle : 0.768 8.405 4722 Z= 0.391 Chirality : 0.049 0.280 506 Planarity : 0.005 0.037 611 Dihedral : 5.799 22.682 478 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.96 % Allowed : 27.55 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.64 (0.39), residues: 424 helix: -4.90 (0.20), residues: 28 sheet: 0.49 (0.52), residues: 113 loop : -1.43 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 403 TYR 0.022 0.002 TYR B 508 PHE 0.014 0.002 PHE B 374 TRP 0.021 0.002 TRP B 436 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 ( 3463) covalent geometry : angle 0.75657 / 0.39 ( 4707) SS BOND : bond 0.00682 / 0.34 ( 6) SS BOND : angle 2.47847 / 1.34 ( 12) hydrogen bonds : bond 0.03999 / 2.48 ( 102) hydrogen bonds : angle 6.26312 / 4.30 ( 243) link_NAG-ASN : bond 0.00047 / 0.02 ( 1) link_NAG-ASN : angle 2.25132 / 1.10 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1160.96 seconds wall clock time: 20 minutes 39.76 seconds (1239.76 seconds total)