Starting phenix.real_space_refine on Wed Jul 1 23:02:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mkm_23899/07_2026/7mkm_23899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkm_23899/07_2026/7mkm_23899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mkm_23899/07_2026/7mkm_23899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkm_23899/07_2026/7mkm_23899.map" model { file = "/net/cci-nas-00/data/ceres_data/7mkm_23899/07_2026/7mkm_23899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkm_23899/07_2026/7mkm_23899.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mkm_23899/07_2026/7mkm_23899.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mkm_23899/07_2026/7mkm_23899.cif" } resolution = 3.16 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= 0.017 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 751 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 17 5.16 5 C 2030 2.51 5 N 528 2.21 5 O 617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3192 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1500 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 178} Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.94, per 1000 atoms: 0.29 Number of scatterers: 3192 At special positions: 0 Unit cell: (77.72, 67.28, 98.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 617 8.00 N 528 7.00 C 2030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 116.6 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 11.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.810A pdb=" N ASN L 52 " --> pdb=" O ASP L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.100A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (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 3 through 7 removed outlier: 3.734A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.607A pdb=" N GLY H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 37 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN H 39 " --> pdb=" O LYS H 92 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 105 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 3 through 5 removed outlier: 3.771A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 74 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET L 21 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU L 72 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS L 23 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR L 71 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 47 removed outlier: 4.688A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN L 88 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR L 35 " --> pdb=" O TYR L 86 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 198 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: 0.38 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1009 1.34 - 1.46: 881 1.46 - 1.58: 1364 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3276 Sorted by residual: bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.426 -0.020 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.65e-01 bond pdb=" CA MET L 77 " pdb=" CB MET L 77 " ideal model delta sigma weight residual 1.513 1.536 -0.023 2.59e-02 1.49e+03 7.75e-01 bond pdb=" C2 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.439 1.454 -0.015 2.00e-02 2.50e+03 5.78e-01 ... (remaining 3271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 4317 2.13 - 4.25: 132 4.25 - 6.38: 4 6.38 - 8.50: 2 8.50 - 10.63: 2 Bond angle restraints: 4457 Sorted by residual: angle pdb=" C ARG L 76 " pdb=" N MET L 77 " pdb=" CA MET L 77 " ideal model delta sigma weight residual 122.04 130.76 -8.72 2.11e+00 2.25e-01 1.71e+01 angle pdb=" CA ARG L 60 " pdb=" CB ARG L 60 " pdb=" CG ARG L 60 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA LEU H 29 " pdb=" CB LEU H 29 " pdb=" CG LEU H 29 " ideal model delta sigma weight residual 116.30 126.93 -10.63 3.50e+00 8.16e-02 9.23e+00 angle pdb=" C LEU H 67 " pdb=" N SER H 68 " pdb=" CA SER H 68 " ideal model delta sigma weight residual 121.62 126.42 -4.80 1.83e+00 2.99e-01 6.87e+00 angle pdb=" C GLY L 65 " pdb=" N CYS L 66 " pdb=" CA CYS L 66 " ideal model delta sigma weight residual 122.59 126.34 -3.75 1.57e+00 4.06e-01 5.70e+00 ... (remaining 4452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 1732 17.71 - 35.41: 159 35.41 - 53.12: 21 53.12 - 70.82: 0 70.82 - 88.53: 2 Dihedral angle restraints: 1914 sinusoidal: 737 harmonic: 1177 Sorted by residual: dihedral pdb=" CA MET L 77 " pdb=" C MET L 77 " pdb=" N GLU L 78 " pdb=" CA GLU L 78 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR H 59 " pdb=" C TYR H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASP L 81 " pdb=" C ASP L 81 " pdb=" N ALA L 82 " pdb=" CA ALA L 82 " ideal model delta harmonic sigma weight residual -180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 1911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 312 0.037 - 0.074: 113 0.074 - 0.111: 37 0.111 - 0.147: 16 0.147 - 0.184: 2 Chirality restraints: 480 Sorted by residual: chirality pdb=" CB ILE A 402 " pdb=" CA ILE A 402 " pdb=" CG1 ILE A 402 " pdb=" CG2 ILE A 402 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA ILE L 74 " pdb=" N ILE L 74 " pdb=" C ILE L 74 " pdb=" CB ILE L 74 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE L 47 " pdb=" N ILE L 47 " pdb=" C ILE L 47 " pdb=" CB ILE L 47 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 477 not shown) Planarity restraints: 573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO A 491 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.018 2.00e-02 2.50e+03 1.74e-02 3.80e+00 pdb=" CG ASN A 343 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " -0.137 9.50e-02 1.11e+02 6.17e-02 2.96e+00 pdb=" NE ARG A 466 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " -0.000 2.00e-02 2.50e+03 ... (remaining 570 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 130 2.72 - 3.27: 3159 3.27 - 3.81: 4603 3.81 - 4.36: 5272 4.36 - 4.90: 9289 Nonbonded interactions: 22453 Sorted by model distance: nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.274 3.040 nonbonded pdb=" O ASN A 440 " pdb=" ND2 ASN L 91 " model vdw 2.324 3.120 nonbonded pdb=" O ALA A 475 " pdb=" ND2 ASN A 487 " model vdw 2.382 3.120 nonbonded pdb=" OG1 THR A 393 " pdb=" O HIS A 519 " model vdw 2.394 3.040 ... (remaining 22448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.770 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 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 0.031 3282 Z= 0.131 Angle : 0.806 10.631 4470 Z= 0.434 Chirality : 0.047 0.184 480 Planarity : 0.006 0.062 572 Dihedral : 13.139 88.529 1155 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.38), residues: 400 helix: -3.71 (0.45), residues: 32 sheet: 2.48 (0.49), residues: 100 loop : -2.02 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 466 TYR 0.018 0.003 TYR L 85 PHE 0.015 0.002 PHE A 429 TRP 0.022 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 3276) covalent geometry : angle 0.79467 / 0.43 ( 4457) SS BOND : bond 0.00488 / 0.29 ( 5) SS BOND : angle 1.19163 / 0.67 ( 10) hydrogen bonds : bond 0.30388 / 19.08 ( 72) hydrogen bonds : angle 12.10241 / 8.38 ( 198) link_NAG-ASN : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : angle 5.05605 / 2.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.068 Fit side-chains REVERT: A 486 PHE cc_start: 0.6384 (t80) cc_final: 0.6143 (t80) REVERT: L 34 TRP cc_start: 0.4286 (m100) cc_final: 0.4080 (m100) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0427 time to fit residues: 3.1682 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 37 optimal weight: 0.5980 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.201174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.178538 restraints weight = 5170.055| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 2.97 r_work: 0.4332 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3282 Z= 0.140 Angle : 0.719 8.121 4470 Z= 0.389 Chirality : 0.046 0.258 480 Planarity : 0.005 0.055 572 Dihedral : 7.701 26.236 450 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.44 % Allowed : 9.48 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.39), residues: 400 helix: -2.39 (0.85), residues: 26 sheet: 1.64 (0.46), residues: 113 loop : -1.73 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 408 TYR 0.024 0.002 TYR A 423 PHE 0.030 0.002 PHE A 400 TRP 0.020 0.002 TRP A 436 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 3276) covalent geometry : angle 0.71350 / 0.39 ( 4457) SS BOND : bond 0.00531 / 0.26 ( 5) SS BOND : angle 1.17163 / 0.61 ( 10) hydrogen bonds : bond 0.04597 / 2.85 ( 72) hydrogen bonds : angle 8.94640 / 6.28 ( 198) link_NAG-ASN : bond 0.00434 / 0.23 ( 1) link_NAG-ASN : angle 2.89969 / 1.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.124 Fit side-chains REVERT: A 365 TYR cc_start: 0.6363 (m-80) cc_final: 0.5708 (m-80) REVERT: A 465 GLU cc_start: 0.6812 (tp30) cc_final: 0.6380 (tp30) REVERT: A 466 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7323 (mtm-85) REVERT: A 486 PHE cc_start: 0.7045 (t80) cc_final: 0.6546 (t80) REVERT: L 68 THR cc_start: 0.7257 (OUTLIER) cc_final: 0.7052 (m) REVERT: L 86 TYR cc_start: 0.5464 (m-10) cc_final: 0.5100 (m-10) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.0783 time to fit residues: 5.7572 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 0.0470 chunk 22 optimal weight: 0.0070 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN H 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.199552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.176674 restraints weight = 5110.086| |-----------------------------------------------------------------------------| r_work (start): 0.4402 rms_B_bonded: 3.03 r_work: 0.4304 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3282 Z= 0.133 Angle : 0.671 8.363 4470 Z= 0.363 Chirality : 0.045 0.261 480 Planarity : 0.005 0.052 572 Dihedral : 6.953 27.549 450 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.01 % Allowed : 12.36 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.39), residues: 400 helix: -1.84 (1.03), residues: 27 sheet: 1.05 (0.45), residues: 115 loop : -1.71 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.011 0.002 TYR A 453 PHE 0.012 0.002 PHE A 400 TRP 0.025 0.002 TRP H 36 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 3276) covalent geometry : angle 0.66742 / 0.36 ( 4457) SS BOND : bond 0.00483 / 0.25 ( 5) SS BOND : angle 0.99179 / 0.51 ( 10) hydrogen bonds : bond 0.04500 / 2.76 ( 72) hydrogen bonds : angle 7.93437 / 5.57 ( 198) link_NAG-ASN : bond 0.00255 / 0.13 ( 1) link_NAG-ASN : angle 2.51261 / 1.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.118 Fit side-chains REVERT: A 365 TYR cc_start: 0.6427 (m-80) cc_final: 0.5747 (m-80) REVERT: A 465 GLU cc_start: 0.7146 (tp30) cc_final: 0.6761 (tp30) REVERT: A 486 PHE cc_start: 0.6978 (t80) cc_final: 0.6532 (t80) REVERT: L 68 THR cc_start: 0.6936 (m) cc_final: 0.6691 (m) outliers start: 7 outliers final: 2 residues processed: 58 average time/residue: 0.0697 time to fit residues: 4.9179 Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.4980 chunk 13 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.192793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.171668 restraints weight = 5141.190| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 2.69 r_work: 0.4272 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3282 Z= 0.160 Angle : 0.697 8.538 4470 Z= 0.376 Chirality : 0.046 0.252 480 Planarity : 0.005 0.052 572 Dihedral : 6.923 27.469 450 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.72 % Allowed : 14.37 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.39), residues: 400 helix: -1.96 (1.01), residues: 27 sheet: 0.49 (0.44), residues: 113 loop : -1.74 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 355 TYR 0.014 0.002 TYR H 58 PHE 0.011 0.002 PHE A 497 TRP 0.025 0.003 TRP H 47 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 3276) covalent geometry : angle 0.69240 / 0.38 ( 4457) SS BOND : bond 0.00564 / 0.29 ( 5) SS BOND : angle 1.08541 / 0.57 ( 10) hydrogen bonds : bond 0.04797 / 2.99 ( 72) hydrogen bonds : angle 7.74389 / 5.46 ( 198) link_NAG-ASN : bond 0.00374 / 0.20 ( 1) link_NAG-ASN : angle 2.77148 / 1.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.087 Fit side-chains REVERT: A 465 GLU cc_start: 0.7084 (tp30) cc_final: 0.6808 (tp30) REVERT: A 466 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7298 (mtm180) REVERT: A 486 PHE cc_start: 0.6785 (t80) cc_final: 0.6436 (t80) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.0642 time to fit residues: 4.0807 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 14 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 0.0070 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.195315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.173541 restraints weight = 5190.285| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.85 r_work: 0.4283 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3282 Z= 0.121 Angle : 0.633 8.307 4470 Z= 0.342 Chirality : 0.044 0.212 480 Planarity : 0.004 0.051 572 Dihedral : 6.418 27.618 450 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.72 % Allowed : 15.23 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.39), residues: 400 helix: -1.91 (1.00), residues: 27 sheet: 0.15 (0.45), residues: 115 loop : -1.69 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 509 TYR 0.012 0.001 TYR A 453 PHE 0.013 0.001 PHE A 400 TRP 0.023 0.002 TRP H 36 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 3276) covalent geometry : angle 0.62958 / 0.34 ( 4457) SS BOND : bond 0.00456 / 0.23 ( 5) SS BOND : angle 1.00418 / 0.51 ( 10) hydrogen bonds : bond 0.03901 / 2.44 ( 72) hydrogen bonds : angle 7.53546 / 5.33 ( 198) link_NAG-ASN : bond 0.00158 / 0.08 ( 1) link_NAG-ASN : angle 2.30561 / 1.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.068 Fit side-chains REVERT: A 465 GLU cc_start: 0.7047 (tp30) cc_final: 0.6776 (tp30) REVERT: A 466 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7260 (mtm-85) REVERT: A 486 PHE cc_start: 0.6801 (t80) cc_final: 0.6455 (t80) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.0557 time to fit residues: 3.4596 Evaluate side-chains 49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.191844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.170595 restraints weight = 5089.594| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 2.69 r_work: 0.4257 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3282 Z= 0.166 Angle : 0.684 8.562 4470 Z= 0.369 Chirality : 0.045 0.227 480 Planarity : 0.005 0.051 572 Dihedral : 6.576 27.708 450 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.44 % Allowed : 16.67 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.39), residues: 400 helix: -1.97 (1.02), residues: 27 sheet: 0.19 (0.47), residues: 110 loop : -1.85 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 66 TYR 0.015 0.002 TYR H 58 PHE 0.011 0.002 PHE A 497 TRP 0.022 0.003 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 ( 3276) covalent geometry : angle 0.67869 / 0.37 ( 4457) SS BOND : bond 0.00548 / 0.28 ( 5) SS BOND : angle 1.09020 / 0.56 ( 10) hydrogen bonds : bond 0.04744 / 2.94 ( 72) hydrogen bonds : angle 7.58082 / 5.34 ( 198) link_NAG-ASN : bond 0.00272 / 0.14 ( 1) link_NAG-ASN : angle 2.79432 / 1.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.081 Fit side-chains REVERT: A 417 LYS cc_start: 0.5850 (mmtt) cc_final: 0.5519 (mmtt) REVERT: A 465 GLU cc_start: 0.6997 (tp30) cc_final: 0.6776 (tp30) REVERT: A 466 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7374 (mtm-85) REVERT: A 486 PHE cc_start: 0.6733 (t80) cc_final: 0.6416 (t80) REVERT: A 509 ARG cc_start: 0.6977 (mtt180) cc_final: 0.6023 (mtp85) outliers start: 5 outliers final: 5 residues processed: 52 average time/residue: 0.0745 time to fit residues: 4.5647 Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.191345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.169661 restraints weight = 5220.794| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.86 r_work: 0.4242 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3282 Z= 0.156 Angle : 0.683 8.384 4470 Z= 0.367 Chirality : 0.045 0.212 480 Planarity : 0.005 0.051 572 Dihedral : 6.491 27.771 450 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.01 % Allowed : 16.95 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.40), residues: 400 helix: -1.95 (1.03), residues: 27 sheet: 0.03 (0.49), residues: 104 loop : -1.96 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 44 TYR 0.018 0.002 TYR L 35 PHE 0.011 0.002 PHE A 400 TRP 0.022 0.003 TRP H 36 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 3276) covalent geometry : angle 0.67866 / 0.37 ( 4457) SS BOND : bond 0.00516 / 0.26 ( 5) SS BOND : angle 1.08109 / 0.56 ( 10) hydrogen bonds : bond 0.04549 / 2.83 ( 72) hydrogen bonds : angle 7.64515 / 5.38 ( 198) link_NAG-ASN : bond 0.00225 / 0.12 ( 1) link_NAG-ASN : angle 2.68470 / 1.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.085 Fit side-chains REVERT: A 465 GLU cc_start: 0.7045 (tp30) cc_final: 0.6829 (tp30) REVERT: A 466 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7453 (mtm-85) REVERT: A 486 PHE cc_start: 0.6738 (t80) cc_final: 0.6421 (t80) REVERT: A 509 ARG cc_start: 0.7001 (mtt180) cc_final: 0.5988 (mtp85) outliers start: 7 outliers final: 7 residues processed: 50 average time/residue: 0.0636 time to fit residues: 3.8708 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.0060 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.0000 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 0.0020 overall best weight: 0.1706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.195436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.173918 restraints weight = 5173.140| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.87 r_work: 0.4293 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3282 Z= 0.113 Angle : 0.631 8.158 4470 Z= 0.337 Chirality : 0.043 0.158 480 Planarity : 0.004 0.046 572 Dihedral : 5.892 26.795 450 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.72 % Allowed : 16.38 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.40), residues: 400 helix: -1.83 (1.05), residues: 27 sheet: 0.19 (0.51), residues: 101 loop : -1.84 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 100 TYR 0.012 0.001 TYR L 35 PHE 0.012 0.001 PHE A 400 TRP 0.024 0.002 TRP H 36 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 3276) covalent geometry : angle 0.62807 / 0.34 ( 4457) SS BOND : bond 0.00448 / 0.21 ( 5) SS BOND : angle 1.12699 / 0.54 ( 10) hydrogen bonds : bond 0.03386 / 2.11 ( 72) hydrogen bonds : angle 7.40216 / 5.24 ( 198) link_NAG-ASN : bond 0.00016 / 0.01 ( 1) link_NAG-ASN : angle 1.92648 / 0.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.118 Fit side-chains REVERT: A 466 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.7395 (mtm-85) REVERT: A 486 PHE cc_start: 0.6679 (t80) cc_final: 0.6420 (t80) REVERT: H 103 ASP cc_start: 0.7573 (t0) cc_final: 0.7255 (m-30) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.0707 time to fit residues: 4.2347 Evaluate side-chains 45 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.191928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.170681 restraints weight = 5184.167| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 2.76 r_work: 0.4257 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3282 Z= 0.160 Angle : 0.702 8.449 4470 Z= 0.377 Chirality : 0.045 0.186 480 Planarity : 0.005 0.048 572 Dihedral : 6.202 26.566 450 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.30 % Allowed : 15.80 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.40), residues: 400 helix: -1.91 (1.04), residues: 27 sheet: -0.02 (0.51), residues: 105 loop : -1.86 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 97 TYR 0.016 0.002 TYR L 35 PHE 0.012 0.002 PHE A 497 TRP 0.022 0.003 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 3276) covalent geometry : angle 0.69776 / 0.38 ( 4457) SS BOND : bond 0.00492 / 0.26 ( 5) SS BOND : angle 1.07991 / 0.57 ( 10) hydrogen bonds : bond 0.04489 / 2.76 ( 72) hydrogen bonds : angle 7.51301 / 5.25 ( 198) link_NAG-ASN : bond 0.00156 / 0.08 ( 1) link_NAG-ASN : angle 2.60099 / 1.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.115 Fit side-chains REVERT: A 465 GLU cc_start: 0.6788 (tp30) cc_final: 0.6513 (tp30) REVERT: A 466 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7323 (mtm-85) REVERT: A 486 PHE cc_start: 0.6688 (t80) cc_final: 0.6394 (t80) REVERT: A 509 ARG cc_start: 0.7020 (mtt180) cc_final: 0.6050 (mtp180) REVERT: H 103 ASP cc_start: 0.7695 (t0) cc_final: 0.7413 (m-30) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.0827 time to fit residues: 5.0007 Evaluate side-chains 48 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.0010 chunk 15 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 GLN L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.192502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.171330 restraints weight = 5116.965| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.76 r_work: 0.4264 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3282 Z= 0.143 Angle : 0.690 8.336 4470 Z= 0.369 Chirality : 0.044 0.157 480 Planarity : 0.005 0.048 572 Dihedral : 6.133 26.731 450 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.01 % Allowed : 16.38 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.41), residues: 400 helix: -1.92 (1.03), residues: 27 sheet: -0.14 (0.51), residues: 107 loop : -1.86 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 408 TYR 0.017 0.002 TYR L 35 PHE 0.010 0.002 PHE A 347 TRP 0.020 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 3276) covalent geometry : angle 0.68615 / 0.37 ( 4457) SS BOND : bond 0.00458 / 0.23 ( 5) SS BOND : angle 1.06276 / 0.54 ( 10) hydrogen bonds : bond 0.04102 / 2.51 ( 72) hydrogen bonds : angle 7.48059 / 5.23 ( 198) link_NAG-ASN : bond 0.00137 / 0.07 ( 1) link_NAG-ASN : angle 2.50809 / 1.24 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 465 GLU cc_start: 0.6963 (tp30) cc_final: 0.6760 (tp30) REVERT: A 466 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7589 (mtm-85) REVERT: A 486 PHE cc_start: 0.6628 (t80) cc_final: 0.6359 (t80) REVERT: A 509 ARG cc_start: 0.7023 (mtt180) cc_final: 0.6072 (mtp180) REVERT: H 103 ASP cc_start: 0.7672 (t0) cc_final: 0.7366 (m-30) outliers start: 7 outliers final: 7 residues processed: 49 average time/residue: 0.0849 time to fit residues: 4.8917 Evaluate side-chains 49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.189959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.168759 restraints weight = 5207.904| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 2.75 r_work: 0.4237 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3282 Z= 0.196 Angle : 0.739 8.419 4470 Z= 0.396 Chirality : 0.046 0.186 480 Planarity : 0.005 0.050 572 Dihedral : 6.418 26.776 450 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.30 % Allowed : 16.09 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.40), residues: 400 helix: -1.97 (1.04), residues: 27 sheet: -0.20 (0.52), residues: 105 loop : -2.02 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 66 TYR 0.018 0.002 TYR L 35 PHE 0.012 0.002 PHE A 497 TRP 0.016 0.003 TRP A 353 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 ( 3276) covalent geometry : angle 0.73365 / 0.40 ( 4457) SS BOND : bond 0.00586 / 0.30 ( 5) SS BOND : angle 1.22844 / 0.66 ( 10) hydrogen bonds : bond 0.04999 / 3.08 ( 72) hydrogen bonds : angle 7.69040 / 5.35 ( 198) link_NAG-ASN : bond 0.00275 / 0.14 ( 1) link_NAG-ASN : angle 2.92908 / 1.45 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 926.38 seconds wall clock time: 16 minutes 35.55 seconds (995.55 seconds total)