Starting phenix.real_space_refine on Sun Apr 27 09:09:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8idn_35369/04_2025/8idn_35369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8idn_35369/04_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_35369/04_2025/8idn_35369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8idn_35369/04_2025/8idn_35369.map" model { file = "/net/cci-nas-00/data/ceres_data/8idn_35369/04_2025/8idn_35369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8idn_35369/04_2025/8idn_35369.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 3.31, per 1000 atoms: 1.01 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: 0.95 Conformation dependent library (CDL) restraints added in 397.6 milliseconds 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: 0.46 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: 0.86 Time building geometry restraints manager: 1.11 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: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.040 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP H 127 HIS 0.000 0.000 HIS L 116 PHE 0.016 0.001 PHE A 347 TYR 0.010 0.001 TYR A 505 ARG 0.004 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 1) link_NAG-ASN : angle 2.08253 ( 3) link_BETA1-4 : bond 0.00329 ( 2) link_BETA1-4 : angle 2.11182 ( 6) link_ALPHA1-3 : bond 0.00321 ( 1) link_ALPHA1-3 : angle 1.70239 ( 3) hydrogen bonds : bond 0.27898 ( 108) hydrogen bonds : angle 10.09339 ( 264) SS BOND : bond 0.00259 ( 6) SS BOND : angle 1.21775 ( 12) covalent geometry : bond 0.00284 ( 3373) covalent geometry : angle 0.57889 ( 4595) *********************** 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 : 0.336 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: 0.1684 time to fit residues: 16.0610 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 : 0.361 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.190824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.148650 restraints weight = 4115.667| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.43 r_work: 0.3706 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3383 Z= 0.139 Angle : 0.607 6.730 4619 Z= 0.325 Chirality : 0.046 0.197 519 Planarity : 0.004 0.036 584 Dihedral : 10.572 75.166 540 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.63 % Favored : 96.13 % Rotamer: Outliers : 1.13 % Allowed : 9.89 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.42), residues: 413 helix: -1.63 (1.05), residues: 27 sheet: 1.37 (0.43), residues: 145 loop : -0.69 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.002 0.000 HIS L 63 PHE 0.010 0.001 PHE L 65 TYR 0.008 0.001 TYR A 508 ARG 0.004 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 1) link_NAG-ASN : angle 2.21762 ( 3) link_BETA1-4 : bond 0.00390 ( 2) link_BETA1-4 : angle 2.25696 ( 6) link_ALPHA1-3 : bond 0.00684 ( 1) link_ALPHA1-3 : angle 2.43376 ( 3) hydrogen bonds : bond 0.05475 ( 108) hydrogen bonds : angle 7.09602 ( 264) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.92972 ( 12) covalent geometry : bond 0.00301 ( 3373) covalent geometry : angle 0.59552 ( 4595) *********************** 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 76 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7779 (m-30) cc_final: 0.7533 (m-30) REVERT: A 509 ARG cc_start: 0.7314 (mtt90) cc_final: 0.6944 (mtt90) REVERT: H 69 MET cc_start: 0.8308 (tpp) cc_final: 0.7885 (ttm) REVERT: L 75 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7777 (mtp-110) outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.1588 time to fit residues: 14.3533 Evaluate side-chains 68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 107 ILE 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 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.189402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.146337 restraints weight = 4114.099| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.76 r_work: 0.3680 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3383 Z= 0.138 Angle : 0.584 6.069 4619 Z= 0.306 Chirality : 0.045 0.181 519 Planarity : 0.004 0.051 584 Dihedral : 9.343 61.451 538 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 1.69 % Allowed : 13.56 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.42), residues: 413 helix: -1.73 (1.02), residues: 27 sheet: 1.40 (0.43), residues: 144 loop : -0.73 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 66 HIS 0.002 0.001 HIS L 63 PHE 0.011 0.001 PHE L 65 TYR 0.010 0.001 TYR H 113 ARG 0.003 0.000 ARG H 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 1) link_NAG-ASN : angle 2.13344 ( 3) link_BETA1-4 : bond 0.00343 ( 2) link_BETA1-4 : angle 2.22985 ( 6) link_ALPHA1-3 : bond 0.00969 ( 1) link_ALPHA1-3 : angle 1.82769 ( 3) hydrogen bonds : bond 0.04479 ( 108) hydrogen bonds : angle 6.50633 ( 264) SS BOND : bond 0.00330 ( 6) SS BOND : angle 0.82133 ( 12) covalent geometry : bond 0.00309 ( 3373) covalent geometry : angle 0.57380 ( 4595) *********************** 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: 6 poor density : 69 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 505 TYR cc_start: 0.6947 (m-10) cc_final: 0.6503 (m-80) REVERT: H 69 MET cc_start: 0.8325 (tpp) cc_final: 0.8025 (ttm) outliers start: 6 outliers final: 3 residues processed: 73 average time/residue: 0.2329 time to fit residues: 20.7837 Evaluate side-chains 65 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.191604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.149508 restraints weight = 4208.587| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 4.01 r_work: 0.3697 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3383 Z= 0.107 Angle : 0.571 7.351 4619 Z= 0.292 Chirality : 0.044 0.171 519 Planarity : 0.004 0.044 584 Dihedral : 7.547 44.179 536 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 1.69 % Allowed : 16.10 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.42), residues: 413 helix: -1.92 (0.98), residues: 27 sheet: 1.32 (0.43), residues: 145 loop : -0.77 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.001 0.000 HIS L 116 PHE 0.009 0.001 PHE L 65 TYR 0.009 0.001 TYR A 505 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 1) link_NAG-ASN : angle 2.08258 ( 3) link_BETA1-4 : bond 0.00370 ( 2) link_BETA1-4 : angle 2.04950 ( 6) link_ALPHA1-3 : bond 0.00937 ( 1) link_ALPHA1-3 : angle 1.76282 ( 3) hydrogen bonds : bond 0.03755 ( 108) hydrogen bonds : angle 6.12383 ( 264) SS BOND : bond 0.00336 ( 6) SS BOND : angle 0.79594 ( 12) covalent geometry : bond 0.00233 ( 3373) covalent geometry : angle 0.56188 ( 4595) *********************** 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 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.650 Fit side-chains REVERT: H 69 MET cc_start: 0.8228 (tpp) cc_final: 0.7988 (ttm) outliers start: 6 outliers final: 6 residues processed: 68 average time/residue: 0.2185 time to fit residues: 18.9029 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN H 54 ASN H 123 GLN L 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.186475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.144022 restraints weight = 4208.330| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 3.77 r_work: 0.3619 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3383 Z= 0.200 Angle : 0.635 6.756 4619 Z= 0.326 Chirality : 0.046 0.174 519 Planarity : 0.005 0.040 584 Dihedral : 7.296 47.383 536 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.60 % Favored : 95.16 % Rotamer: Outliers : 3.11 % Allowed : 14.69 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.42), residues: 413 helix: -1.96 (0.98), residues: 27 sheet: 1.11 (0.43), residues: 145 loop : -0.93 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 127 HIS 0.001 0.000 HIS L 116 PHE 0.014 0.001 PHE L 83 TYR 0.034 0.002 TYR L 53 ARG 0.007 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 1) link_NAG-ASN : angle 2.24899 ( 3) link_BETA1-4 : bond 0.00373 ( 2) link_BETA1-4 : angle 2.23167 ( 6) link_ALPHA1-3 : bond 0.00928 ( 1) link_ALPHA1-3 : angle 1.73644 ( 3) hydrogen bonds : bond 0.03926 ( 108) hydrogen bonds : angle 6.09639 ( 264) SS BOND : bond 0.00404 ( 6) SS BOND : angle 0.69743 ( 12) covalent geometry : bond 0.00459 ( 3373) covalent geometry : angle 0.62653 ( 4595) *********************** 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 80 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: H 69 MET cc_start: 0.8425 (tpp) cc_final: 0.8170 (ttm) outliers start: 11 outliers final: 8 residues processed: 75 average time/residue: 0.1447 time to fit residues: 13.5901 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 : 0.371 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.185745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143738 restraints weight = 4320.778| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.80 r_work: 0.3612 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3383 Z= 0.169 Angle : 0.609 6.672 4619 Z= 0.315 Chirality : 0.045 0.172 519 Planarity : 0.004 0.039 584 Dihedral : 6.914 47.410 536 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.82 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.42), residues: 413 helix: -1.98 (0.99), residues: 27 sheet: 0.93 (0.43), residues: 150 loop : -0.94 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 127 HIS 0.001 0.000 HIS L 116 PHE 0.012 0.001 PHE L 65 TYR 0.031 0.002 TYR L 53 ARG 0.004 0.000 ARG L 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 1) link_NAG-ASN : angle 2.32798 ( 3) link_BETA1-4 : bond 0.00344 ( 2) link_BETA1-4 : angle 2.17893 ( 6) link_ALPHA1-3 : bond 0.00965 ( 1) link_ALPHA1-3 : angle 1.76283 ( 3) hydrogen bonds : bond 0.03777 ( 108) hydrogen bonds : angle 6.06850 ( 264) SS BOND : bond 0.00352 ( 6) SS BOND : angle 0.71701 ( 12) covalent geometry : bond 0.00389 ( 3373) covalent geometry : angle 0.59944 ( 4595) *********************** 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 80 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.333 Fit side-chains REVERT: A 471 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7307 (tm-30) REVERT: H 69 MET cc_start: 0.8432 (tpp) cc_final: 0.8222 (ttm) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.1380 time to fit residues: 12.9120 Evaluate side-chains 76 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 L 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.187984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.146504 restraints weight = 4176.278| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 3.64 r_work: 0.3656 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3383 Z= 0.109 Angle : 0.576 8.280 4619 Z= 0.300 Chirality : 0.044 0.164 519 Planarity : 0.004 0.038 584 Dihedral : 6.145 44.201 536 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 2.82 % Allowed : 16.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.42), residues: 413 helix: -1.95 (0.98), residues: 27 sheet: 0.95 (0.43), residues: 150 loop : -0.88 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 127 HIS 0.002 0.001 HIS L 116 PHE 0.013 0.001 PHE L 65 TYR 0.022 0.001 TYR L 53 ARG 0.002 0.000 ARG L 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 1) link_NAG-ASN : angle 2.21974 ( 3) link_BETA1-4 : bond 0.00331 ( 2) link_BETA1-4 : angle 1.93258 ( 6) link_ALPHA1-3 : bond 0.00986 ( 1) link_ALPHA1-3 : angle 1.69230 ( 3) hydrogen bonds : bond 0.03379 ( 108) hydrogen bonds : angle 5.88598 ( 264) SS BOND : bond 0.00547 ( 6) SS BOND : angle 0.64552 ( 12) covalent geometry : bond 0.00231 ( 3373) covalent geometry : angle 0.56771 ( 4595) *********************** 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 81 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7359 (tm-30) REVERT: A 489 TYR cc_start: 0.7947 (m-10) cc_final: 0.7525 (m-10) REVERT: L 84 SER cc_start: 0.8037 (t) cc_final: 0.7723 (t) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.1427 time to fit residues: 13.6680 Evaluate side-chains 72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.187328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.145378 restraints weight = 4188.465| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.13 r_work: 0.3651 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3383 Z= 0.128 Angle : 0.600 8.277 4619 Z= 0.309 Chirality : 0.045 0.167 519 Planarity : 0.004 0.040 584 Dihedral : 5.897 44.773 536 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.36 % Favored : 95.40 % Rotamer: Outliers : 2.54 % Allowed : 15.82 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.42), residues: 413 helix: -1.99 (0.97), residues: 27 sheet: 0.90 (0.43), residues: 150 loop : -0.88 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 127 HIS 0.001 0.000 HIS L 116 PHE 0.012 0.001 PHE L 65 TYR 0.022 0.001 TYR L 53 ARG 0.002 0.000 ARG L 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 1) link_NAG-ASN : angle 2.24680 ( 3) link_BETA1-4 : bond 0.00365 ( 2) link_BETA1-4 : angle 1.96168 ( 6) link_ALPHA1-3 : bond 0.00917 ( 1) link_ALPHA1-3 : angle 1.58037 ( 3) hydrogen bonds : bond 0.03395 ( 108) hydrogen bonds : angle 5.88609 ( 264) SS BOND : bond 0.00335 ( 6) SS BOND : angle 0.56180 ( 12) covalent geometry : bond 0.00286 ( 3373) covalent geometry : angle 0.59244 ( 4595) *********************** 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 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7373 (tm-30) REVERT: A 489 TYR cc_start: 0.8044 (m-10) cc_final: 0.7560 (m-10) REVERT: L 84 SER cc_start: 0.8001 (t) cc_final: 0.7711 (t) outliers start: 9 outliers final: 8 residues processed: 70 average time/residue: 0.1448 time to fit residues: 12.6454 Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.186669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.145000 restraints weight = 4226.824| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.14 r_work: 0.3645 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3383 Z= 0.137 Angle : 0.613 8.199 4619 Z= 0.314 Chirality : 0.045 0.167 519 Planarity : 0.004 0.040 584 Dihedral : 5.724 45.729 536 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.60 % Favored : 95.16 % Rotamer: Outliers : 2.82 % Allowed : 15.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.42), residues: 413 helix: -1.96 (0.97), residues: 27 sheet: 0.88 (0.43), residues: 150 loop : -0.87 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 127 HIS 0.001 0.001 HIS L 116 PHE 0.012 0.001 PHE L 65 TYR 0.024 0.001 TYR L 53 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 1) link_NAG-ASN : angle 2.24183 ( 3) link_BETA1-4 : bond 0.00238 ( 2) link_BETA1-4 : angle 2.17048 ( 6) link_ALPHA1-3 : bond 0.00986 ( 1) link_ALPHA1-3 : angle 1.54703 ( 3) hydrogen bonds : bond 0.03398 ( 108) hydrogen bonds : angle 5.85287 ( 264) SS BOND : bond 0.00328 ( 6) SS BOND : angle 0.57069 ( 12) covalent geometry : bond 0.00310 ( 3373) covalent geometry : angle 0.60461 ( 4595) *********************** 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 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.386 Fit side-chains REVERT: A 471 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7384 (tm-30) REVERT: A 489 TYR cc_start: 0.8058 (m-10) cc_final: 0.7576 (m-10) REVERT: L 84 SER cc_start: 0.8004 (t) cc_final: 0.7736 (t) outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 0.1519 time to fit residues: 13.2534 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 : 0.346 ------------------------------------------------------------------------------- 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 0 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.146608 restraints weight = 4208.916| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.19 r_work: 0.3653 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2346 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 : 0.596 8.576 4619 Z= 0.305 Chirality : 0.044 0.163 519 Planarity : 0.004 0.041 584 Dihedral : 5.470 44.392 536 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 2.26 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.42), residues: 413 helix: -1.93 (0.98), residues: 27 sheet: 1.06 (0.43), residues: 145 loop : -0.90 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.001 0.001 HIS L 116 PHE 0.013 0.001 PHE L 65 TYR 0.022 0.001 TYR L 53 ARG 0.003 0.000 ARG L 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 1) link_NAG-ASN : angle 2.21746 ( 3) link_BETA1-4 : bond 0.00298 ( 2) link_BETA1-4 : angle 1.98152 ( 6) link_ALPHA1-3 : bond 0.00969 ( 1) link_ALPHA1-3 : angle 1.44503 ( 3) hydrogen bonds : bond 0.03190 ( 108) hydrogen bonds : angle 5.79150 ( 264) SS BOND : bond 0.00249 ( 6) SS BOND : angle 0.62231 ( 12) covalent geometry : bond 0.00243 ( 3373) covalent geometry : angle 0.58869 ( 4595) ********************** 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 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.354 Fit side-chains REVERT: A 471 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7413 (tm-30) REVERT: A 489 TYR cc_start: 0.8063 (m-10) cc_final: 0.7592 (m-10) REVERT: L 84 SER cc_start: 0.7971 (t) cc_final: 0.7715 (t) outliers start: 8 outliers final: 7 residues processed: 66 average time/residue: 0.1390 time to fit residues: 11.5088 Evaluate side-chains 70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 0.0470 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4363 r_free = 0.4363 target = 0.188985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.146857 restraints weight = 4182.097| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 3.15 r_work: 0.3674 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2397 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= 0.112 Angle : 0.592 8.643 4619 Z= 0.305 Chirality : 0.044 0.194 519 Planarity : 0.004 0.041 584 Dihedral : 5.286 43.844 536 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.36 % Favored : 95.40 % Rotamer: Outliers : 2.26 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.42), residues: 413 helix: -1.90 (0.98), residues: 27 sheet: 0.87 (0.42), residues: 150 loop : -0.80 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS L 116 PHE 0.012 0.001 PHE L 65 TYR 0.021 0.001 TYR L 53 ARG 0.003 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 1) link_NAG-ASN : angle 2.19607 ( 3) link_BETA1-4 : bond 0.00293 ( 2) link_BETA1-4 : angle 1.91016 ( 6) link_ALPHA1-3 : bond 0.00960 ( 1) link_ALPHA1-3 : angle 1.42442 ( 3) hydrogen bonds : bond 0.03277 ( 108) hydrogen bonds : angle 5.84811 ( 264) SS BOND : bond 0.00237 ( 6) SS BOND : angle 0.57066 ( 12) covalent geometry : bond 0.00245 ( 3373) covalent geometry : angle 0.58503 ( 4595) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2317.31 seconds wall clock time: 41 minutes 21.88 seconds (2481.88 seconds total)