Starting phenix.real_space_refine on Fri Aug 22 15:40:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8idn_35369/08_2025/8idn_35369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8idn_35369/08_2025/8idn_35369.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8idn_35369/08_2025/8idn_35369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8idn_35369/08_2025/8idn_35369.map" model { file = "/net/cci-nas-00/data/ceres_data/8idn_35369/08_2025/8idn_35369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8idn_35369/08_2025/8idn_35369.cif" } 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= 0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2169 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2092 2.51 5 N 542 2.21 5 O 644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3292 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.86, per 1000 atoms: 0.26 Number of scatterers: 3292 At special positions: 0 Unit cell: (68.34, 73.7, 87.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 644 8.00 N 542 7.00 C 2092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN H 79 " Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 89.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 11.2% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.214A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 removed outlier: 4.217A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.628A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.871A pdb=" N LYS H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.780A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.746A pdb=" N GLN H 22 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR H 40 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 30 through 31 removed outlier: 7.117A pdb=" N VAL H 53 " --> pdb=" O MET H 69 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N MET H 69 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'L' and resid 28 through 31 removed outlier: 3.515A pdb=" N THR L 126 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE L 106 " --> pdb=" O GLU L 59 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP L 56 " --> pdb=" O LEU L 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 28 through 31 removed outlier: 3.515A pdb=" N THR L 126 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR L 113 " --> pdb=" O HIS L 116 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 264 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: 0.43 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1043 1.35 - 1.47: 913 1.47 - 1.59: 1401 1.59 - 1.71: 0 1.71 - 1.84: 16 Bond restraints: 3373 Sorted by residual: bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.443 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 3368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 4459 1.33 - 2.65: 92 2.65 - 3.98: 29 3.98 - 5.31: 10 5.31 - 6.64: 5 Bond angle restraints: 4595 Sorted by residual: angle pdb=" C ALA L 71 " pdb=" N THR L 72 " pdb=" CA THR L 72 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C3 BMA B 3 " pdb=" C2 BMA B 3 " pdb=" O2 BMA B 3 " ideal model delta sigma weight residual 112.95 106.31 6.64 3.00e+00 1.11e-01 4.89e+00 angle pdb=" CG1 ILE H 49 " pdb=" CB ILE H 49 " pdb=" CG2 ILE H 49 " ideal model delta sigma weight residual 110.70 104.21 6.49 3.00e+00 1.11e-01 4.69e+00 angle pdb=" C3 MAN B 4 " pdb=" C2 MAN B 4 " pdb=" O2 MAN B 4 " ideal model delta sigma weight residual 111.77 105.60 6.17 3.00e+00 1.11e-01 4.23e+00 angle pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sigma weight residual 113.24 107.33 5.91 3.00e+00 1.11e-01 3.88e+00 ... (remaining 4590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.23: 1889 22.23 - 44.46: 111 44.46 - 66.68: 9 66.68 - 88.91: 8 88.91 - 111.14: 4 Dihedral angle restraints: 2021 sinusoidal: 821 harmonic: 1200 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 49.97 43.03 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 177.57 111.14 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -61.70 109.32 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 2018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 421 0.053 - 0.106: 80 0.106 - 0.159: 15 0.159 - 0.212: 0 0.212 - 0.265: 3 Chirality restraints: 519 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE H 49 " pdb=" CA ILE H 49 " pdb=" CG1 ILE H 49 " pdb=" CG2 ILE H 49 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN H 79 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 516 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 463 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 60 " -0.015 5.00e-02 4.00e+02 2.31e-02 8.55e-01 pdb=" N PRO L 61 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 347 " 0.006 2.00e-02 2.50e+03 6.94e-03 8.42e-01 pdb=" CG PHE A 347 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 347 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 347 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 347 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 347 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 347 " 0.001 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 55 2.68 - 3.23: 2959 3.23 - 3.79: 4611 3.79 - 4.34: 6491 4.34 - 4.90: 10839 Nonbonded interactions: 24955 Sorted by model distance: nonbonded pdb=" O TYR H 120 " pdb=" OG SER L 74 " model vdw 2.120 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.153 3.040 nonbonded pdb=" O ALA L 71 " pdb=" OG1 THR L 72 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 453 " pdb=" OE1 GLN A 493 " model vdw 2.262 3.040 nonbonded pdb=" O TRP A 353 " pdb=" NH2 ARG A 466 " model vdw 2.321 3.120 ... (remaining 24950 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.020 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.003 0.037 3383 Z= 0.134 Angle : 0.590 6.637 4619 Z= 0.281 Chirality : 0.046 0.265 519 Planarity : 0.003 0.036 584 Dihedral : 14.934 111.141 1243 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.36 % Favored : 95.40 % Rotamer: Outliers : 0.56 % Allowed : 0.56 % Favored : 98.87 % 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 aren not related in a simple way. whole: -0.05 (0.42), residues: 413 helix: -1.63 (1.06), residues: 27 sheet: 1.39 (0.44), residues: 146 loop : -0.79 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 346 TYR 0.010 0.001 TYR A 505 PHE 0.016 0.001 PHE A 347 TRP 0.006 0.001 TRP H 127 HIS 0.000 0.000 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3373) covalent geometry : angle 0.57889 ( 4595) SS BOND : bond 0.00259 ( 6) SS BOND : angle 1.21775 ( 12) hydrogen bonds : bond 0.27898 ( 108) hydrogen bonds : angle 10.09339 ( 264) link_ALPHA1-3 : bond 0.00321 ( 1) link_ALPHA1-3 : angle 1.70239 ( 3) link_BETA1-4 : bond 0.00329 ( 2) link_BETA1-4 : angle 2.11182 ( 6) link_NAG-ASN : bond 0.00302 ( 1) link_NAG-ASN : angle 2.08253 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.114 Fit side-chains REVERT: A 509 ARG cc_start: 0.6952 (mtt90) cc_final: 0.6531 (mtt90) outliers start: 2 outliers final: 2 residues processed: 77 average time/residue: 0.0539 time to fit residues: 5.1896 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.191701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.148977 restraints weight = 4190.303| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 3.53 r_work: 0.3708 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3383 Z= 0.128 Angle : 0.607 6.982 4619 Z= 0.324 Chirality : 0.046 0.200 519 Planarity : 0.004 0.036 584 Dihedral : 10.572 75.638 540 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.39 % Favored : 96.37 % Rotamer: Outliers : 1.69 % Allowed : 9.60 % Favored : 88.70 % 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 aren not related in a simple way. whole: 0.03 (0.42), residues: 413 helix: -1.63 (1.04), residues: 27 sheet: 1.39 (0.43), residues: 145 loop : -0.67 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 509 TYR 0.008 0.001 TYR A 505 PHE 0.011 0.001 PHE L 65 TRP 0.012 0.001 TRP H 66 HIS 0.001 0.000 HIS L 63 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3373) covalent geometry : angle 0.59500 ( 4595) SS BOND : bond 0.00375 ( 6) SS BOND : angle 0.98440 ( 12) hydrogen bonds : bond 0.05250 ( 108) hydrogen bonds : angle 7.09655 ( 264) link_ALPHA1-3 : bond 0.00767 ( 1) link_ALPHA1-3 : angle 2.48848 ( 3) link_BETA1-4 : bond 0.00388 ( 2) link_BETA1-4 : angle 2.24277 ( 6) link_NAG-ASN : bond 0.00515 ( 1) link_NAG-ASN : angle 2.23367 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7773 (m-30) cc_final: 0.7514 (m-30) REVERT: H 69 MET cc_start: 0.8275 (tpp) cc_final: 0.7851 (ttm) REVERT: L 75 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7864 (mtp-110) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.0687 time to fit residues: 6.2448 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 115 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN L 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.191620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.148204 restraints weight = 4204.618| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.93 r_work: 0.3690 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3383 Z= 0.115 Angle : 0.569 5.953 4619 Z= 0.298 Chirality : 0.044 0.180 519 Planarity : 0.004 0.051 584 Dihedral : 9.240 61.686 538 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.63 % Favored : 96.13 % Rotamer: Outliers : 1.41 % Allowed : 13.28 % Favored : 85.31 % 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 aren not related in a simple way. whole: -0.03 (0.42), residues: 413 helix: -1.77 (1.01), residues: 27 sheet: 1.40 (0.43), residues: 145 loop : -0.74 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.013 0.001 TYR L 53 PHE 0.010 0.001 PHE L 65 TRP 0.010 0.001 TRP H 66 HIS 0.002 0.001 HIS L 63 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 3373) covalent geometry : angle 0.55987 ( 4595) SS BOND : bond 0.00339 ( 6) SS BOND : angle 0.78919 ( 12) hydrogen bonds : bond 0.04330 ( 108) hydrogen bonds : angle 6.52959 ( 264) link_ALPHA1-3 : bond 0.00874 ( 1) link_ALPHA1-3 : angle 1.78599 ( 3) link_BETA1-4 : bond 0.00328 ( 2) link_BETA1-4 : angle 2.14940 ( 6) link_NAG-ASN : bond 0.00329 ( 1) link_NAG-ASN : angle 2.06862 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: H 69 MET cc_start: 0.8329 (tpp) cc_final: 0.8004 (ttm) REVERT: L 75 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7762 (mtp-110) outliers start: 5 outliers final: 2 residues processed: 73 average time/residue: 0.0600 time to fit residues: 5.2884 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 29 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.0050 chunk 27 optimal weight: 2.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 ASN H 123 GLN L 73 ASN L 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.185496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.142760 restraints weight = 4184.193| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.24 r_work: 0.3624 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3383 Z= 0.202 Angle : 0.651 6.902 4619 Z= 0.332 Chirality : 0.046 0.173 519 Planarity : 0.005 0.045 584 Dihedral : 8.116 49.298 536 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.33 % Favored : 94.43 % Rotamer: Outliers : 2.26 % Allowed : 14.69 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.42), residues: 413 helix: -1.85 (1.00), residues: 27 sheet: 1.20 (0.43), residues: 143 loop : -0.99 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 357 TYR 0.027 0.002 TYR L 53 PHE 0.017 0.001 PHE L 83 TRP 0.011 0.002 TRP H 66 HIS 0.002 0.001 HIS L 63 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 3373) covalent geometry : angle 0.64108 ( 4595) SS BOND : bond 0.00468 ( 6) SS BOND : angle 0.93946 ( 12) hydrogen bonds : bond 0.04224 ( 108) hydrogen bonds : angle 6.28945 ( 264) link_ALPHA1-3 : bond 0.01022 ( 1) link_ALPHA1-3 : angle 1.72283 ( 3) link_BETA1-4 : bond 0.00396 ( 2) link_BETA1-4 : angle 2.35701 ( 6) link_NAG-ASN : bond 0.00064 ( 1) link_NAG-ASN : angle 2.34275 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.117 Fit side-chains REVERT: H 69 MET cc_start: 0.8449 (tpp) cc_final: 0.8198 (ttm) outliers start: 8 outliers final: 8 residues processed: 75 average time/residue: 0.0600 time to fit residues: 5.5398 Evaluate side-chains 74 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 115 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 73 ASN L 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.186020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.144088 restraints weight = 4237.607| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 3.76 r_work: 0.3628 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3383 Z= 0.158 Angle : 0.612 7.410 4619 Z= 0.315 Chirality : 0.046 0.170 519 Planarity : 0.004 0.042 584 Dihedral : 7.371 47.392 536 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 2.82 % Allowed : 14.41 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.42), residues: 413 helix: -2.07 (0.95), residues: 27 sheet: 0.90 (0.43), residues: 150 loop : -0.95 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 509 TYR 0.014 0.002 TYR L 53 PHE 0.010 0.001 PHE L 83 TRP 0.009 0.002 TRP L 117 HIS 0.002 0.001 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3373) covalent geometry : angle 0.60254 ( 4595) SS BOND : bond 0.00421 ( 6) SS BOND : angle 0.68356 ( 12) hydrogen bonds : bond 0.03770 ( 108) hydrogen bonds : angle 6.14333 ( 264) link_ALPHA1-3 : bond 0.00881 ( 1) link_ALPHA1-3 : angle 1.73329 ( 3) link_BETA1-4 : bond 0.00340 ( 2) link_BETA1-4 : angle 2.19418 ( 6) link_NAG-ASN : bond 0.00242 ( 1) link_NAG-ASN : angle 2.36725 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7283 (tm-30) REVERT: H 69 MET cc_start: 0.8435 (tpp) cc_final: 0.8229 (ttm) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.0581 time to fit residues: 5.3485 Evaluate side-chains 74 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 115 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.1980 chunk 1 optimal weight: 0.1980 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 73 ASN L 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.145390 restraints weight = 4227.076| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 3.08 r_work: 0.3677 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3383 Z= 0.105 Angle : 0.572 8.291 4619 Z= 0.296 Chirality : 0.044 0.163 519 Planarity : 0.004 0.039 584 Dihedral : 6.531 44.270 536 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 3.39 % Allowed : 15.25 % Favored : 81.36 % 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 aren not related in a simple way. whole: -0.43 (0.42), residues: 413 helix: -2.03 (0.95), residues: 27 sheet: 0.91 (0.42), residues: 150 loop : -0.88 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.015 0.001 TYR L 53 PHE 0.011 0.001 PHE L 65 TRP 0.010 0.001 TRP L 117 HIS 0.002 0.000 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 3373) covalent geometry : angle 0.56296 ( 4595) SS BOND : bond 0.00350 ( 6) SS BOND : angle 0.65337 ( 12) hydrogen bonds : bond 0.03396 ( 108) hydrogen bonds : angle 5.96220 ( 264) link_ALPHA1-3 : bond 0.01058 ( 1) link_ALPHA1-3 : angle 1.75583 ( 3) link_BETA1-4 : bond 0.00414 ( 2) link_BETA1-4 : angle 1.98454 ( 6) link_NAG-ASN : bond 0.00373 ( 1) link_NAG-ASN : angle 2.24174 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.127 Fit side-chains REVERT: A 471 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7316 (tm-30) REVERT: A 489 TYR cc_start: 0.7995 (m-10) cc_final: 0.7637 (m-10) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 0.0566 time to fit residues: 5.6092 Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0670 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN L 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.186706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.144741 restraints weight = 4276.875| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.12 r_work: 0.3647 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3383 Z= 0.129 Angle : 0.589 8.060 4619 Z= 0.302 Chirality : 0.045 0.169 519 Planarity : 0.004 0.039 584 Dihedral : 6.171 44.944 536 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 3.11 % Allowed : 15.82 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.42), residues: 413 helix: -2.00 (0.96), residues: 27 sheet: 0.86 (0.42), residues: 150 loop : -0.87 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.015 0.001 TYR L 53 PHE 0.014 0.001 PHE L 65 TRP 0.009 0.001 TRP H 127 HIS 0.002 0.001 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3373) covalent geometry : angle 0.58114 ( 4595) SS BOND : bond 0.00379 ( 6) SS BOND : angle 0.64845 ( 12) hydrogen bonds : bond 0.03447 ( 108) hydrogen bonds : angle 5.91667 ( 264) link_ALPHA1-3 : bond 0.00966 ( 1) link_ALPHA1-3 : angle 1.65579 ( 3) link_BETA1-4 : bond 0.00391 ( 2) link_BETA1-4 : angle 2.00991 ( 6) link_NAG-ASN : bond 0.00221 ( 1) link_NAG-ASN : angle 2.26485 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 489 TYR cc_start: 0.7939 (m-10) cc_final: 0.7478 (m-10) REVERT: L 84 SER cc_start: 0.8054 (t) cc_final: 0.7746 (t) outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 0.0464 time to fit residues: 4.2923 Evaluate side-chains 74 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 115 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.0020 chunk 27 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN L 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.188432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.146722 restraints weight = 4264.425| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.17 r_work: 0.3667 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3383 Z= 0.102 Angle : 0.582 8.349 4619 Z= 0.300 Chirality : 0.044 0.163 519 Planarity : 0.004 0.042 584 Dihedral : 5.678 43.195 536 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 2.54 % Allowed : 15.54 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.42), residues: 413 helix: -1.94 (0.96), residues: 27 sheet: 0.86 (0.42), residues: 150 loop : -0.80 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.014 0.001 TYR L 53 PHE 0.016 0.001 PHE L 65 TRP 0.008 0.001 TRP H 127 HIS 0.004 0.001 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 3373) covalent geometry : angle 0.57449 ( 4595) SS BOND : bond 0.00354 ( 6) SS BOND : angle 0.53969 ( 12) hydrogen bonds : bond 0.03204 ( 108) hydrogen bonds : angle 5.80578 ( 264) link_ALPHA1-3 : bond 0.00996 ( 1) link_ALPHA1-3 : angle 1.63736 ( 3) link_BETA1-4 : bond 0.00403 ( 2) link_BETA1-4 : angle 1.84821 ( 6) link_NAG-ASN : bond 0.00342 ( 1) link_NAG-ASN : angle 2.18292 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 489 TYR cc_start: 0.8039 (m-10) cc_final: 0.7615 (m-10) REVERT: L 84 SER cc_start: 0.7986 (t) cc_final: 0.7702 (t) outliers start: 9 outliers final: 9 residues processed: 76 average time/residue: 0.0564 time to fit residues: 5.2893 Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN L 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.188516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.146333 restraints weight = 4212.944| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 3.32 r_work: 0.3654 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3383 Z= 0.112 Angle : 0.588 8.239 4619 Z= 0.302 Chirality : 0.044 0.165 519 Planarity : 0.004 0.041 584 Dihedral : 5.406 43.603 536 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.36 % Favored : 95.40 % Rotamer: Outliers : 3.11 % Allowed : 16.67 % Favored : 80.23 % 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 aren not related in a simple way. whole: -0.39 (0.42), residues: 413 helix: -1.98 (0.96), residues: 27 sheet: 0.87 (0.42), residues: 150 loop : -0.81 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 82 TYR 0.014 0.001 TYR L 53 PHE 0.013 0.001 PHE L 65 TRP 0.009 0.001 TRP H 127 HIS 0.002 0.001 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3373) covalent geometry : angle 0.58077 ( 4595) SS BOND : bond 0.00329 ( 6) SS BOND : angle 0.50864 ( 12) hydrogen bonds : bond 0.03155 ( 108) hydrogen bonds : angle 5.75611 ( 264) link_ALPHA1-3 : bond 0.01016 ( 1) link_ALPHA1-3 : angle 1.53280 ( 3) link_BETA1-4 : bond 0.00235 ( 2) link_BETA1-4 : angle 2.07969 ( 6) link_NAG-ASN : bond 0.00202 ( 1) link_NAG-ASN : angle 2.11548 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.128 Fit side-chains REVERT: A 471 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7430 (tm-30) REVERT: A 489 TYR cc_start: 0.8042 (m-10) cc_final: 0.7609 (m-10) REVERT: L 84 SER cc_start: 0.7997 (t) cc_final: 0.7737 (t) outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 0.0629 time to fit residues: 5.5962 Evaluate side-chains 72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 439 ASN ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN L 100 GLN L 115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.146789 restraints weight = 4209.516| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 3.21 r_work: 0.3671 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3383 Z= 0.123 Angle : 0.592 8.243 4619 Z= 0.304 Chirality : 0.044 0.164 519 Planarity : 0.004 0.040 584 Dihedral : 5.333 44.117 536 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 3.39 % Allowed : 16.67 % Favored : 79.94 % 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 aren not related in a simple way. whole: -0.41 (0.42), residues: 413 helix: -1.95 (0.97), residues: 27 sheet: 1.05 (0.43), residues: 145 loop : -0.93 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.017 0.001 TYR L 53 PHE 0.013 0.001 PHE L 65 TRP 0.009 0.001 TRP H 127 HIS 0.001 0.000 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3373) covalent geometry : angle 0.58423 ( 4595) SS BOND : bond 0.00178 ( 6) SS BOND : angle 0.63113 ( 12) hydrogen bonds : bond 0.03165 ( 108) hydrogen bonds : angle 5.73200 ( 264) link_ALPHA1-3 : bond 0.00999 ( 1) link_ALPHA1-3 : angle 1.42903 ( 3) link_BETA1-4 : bond 0.00256 ( 2) link_BETA1-4 : angle 1.99068 ( 6) link_NAG-ASN : bond 0.00179 ( 1) link_NAG-ASN : angle 2.14633 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.128 Fit side-chains REVERT: A 471 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7447 (tm-30) REVERT: A 489 TYR cc_start: 0.8045 (m-10) cc_final: 0.7576 (m-10) REVERT: L 84 SER cc_start: 0.7991 (t) cc_final: 0.7731 (t) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.0498 time to fit residues: 4.6997 Evaluate side-chains 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 115 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.188103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.146739 restraints weight = 4304.593| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.22 r_work: 0.3667 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 3383 Z= 0.199 Angle : 1.285 59.198 4619 Z= 0.776 Chirality : 0.054 0.690 519 Planarity : 0.007 0.086 584 Dihedral : 5.425 44.124 536 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 2.54 % Allowed : 17.23 % Favored : 80.23 % Cbeta Deviations : 0.26 % 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 aren not related in a simple way. whole: -0.42 (0.42), residues: 413 helix: -1.95 (0.97), residues: 27 sheet: 1.03 (0.43), residues: 146 loop : -0.95 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.015 0.001 TYR L 53 PHE 0.013 0.001 PHE L 65 TRP 0.009 0.001 TRP H 127 HIS 0.005 0.001 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3373) covalent geometry : angle 1.27023 ( 4595) SS BOND : bond 0.02267 ( 6) SS BOND : angle 3.72620 ( 12) hydrogen bonds : bond 0.03221 ( 108) hydrogen bonds : angle 5.71627 ( 264) link_ALPHA1-3 : bond 0.00500 ( 1) link_ALPHA1-3 : angle 1.09419 ( 3) link_BETA1-4 : bond 0.00370 ( 2) link_BETA1-4 : angle 2.05861 ( 6) link_NAG-ASN : bond 0.00181 ( 1) link_NAG-ASN : angle 2.14555 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 975.51 seconds wall clock time: 17 minutes 17.39 seconds (1037.39 seconds total)