Starting phenix.real_space_refine on Tue Feb 11 22:22:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x96_33068/02_2025/7x96_33068_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x96_33068/02_2025/7x96_33068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x96_33068/02_2025/7x96_33068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x96_33068/02_2025/7x96_33068.map" model { file = "/net/cci-nas-00/data/ceres_data/7x96_33068/02_2025/7x96_33068_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x96_33068/02_2025/7x96_33068_trim.cif" } resolution = 3.4 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 17 5.16 5 C 2159 2.51 5 N 556 2.21 5 O 670 1.98 5 H 3184 0.53 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-5592/modules/chem_data/mon_lib" Total number of atoms: 6586 Number of models: 1 Model: "" Number of chains: 4 Chain: "G" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3065 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1826 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1624 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.69, per 1000 atoms: 0.56 Number of scatterers: 6586 At special positions: 0 Unit cell: (72.123, 86.216, 92.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 O 670 8.00 N 556 7.00 C 2159 6.00 H 3184 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 ALPHA1-3 " BMA A 3 " - " MAN A 4 " ALPHA1-6 " BMA A 3 " - " MAN A 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " BETA1-6 " NAG A 1 " - " FUC A 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 636.5 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 12 sheets defined 14.3% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'G' and resid 337 through 343 Processing helix chain 'G' and resid 364 through 371 removed outlier: 4.481A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 389 Processing helix chain 'G' and resid 403 through 408 removed outlier: 3.922A pdb=" N GLU G 406 " --> pdb=" O ARG G 403 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'G' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.524A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.581A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 90 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.720A pdb=" N CYS G 361 " --> pdb=" O CYS G 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 379 through 380 Processing sheet with id=AA5, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.518A pdb=" N VAL H 116 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA9, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.677A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.563A pdb=" N LEU L 11 " --> pdb=" O LYS L 105 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.563A pdb=" N LEU L 11 " --> pdb=" O LYS L 105 " (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: 2.66 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3183 1.03 - 1.23: 20 1.23 - 1.43: 1514 1.43 - 1.62: 1934 1.62 - 1.82: 21 Bond restraints: 6672 Sorted by residual: bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" C1 MAN A 4 " pdb=" C2 MAN A 4 " ideal model delta sigma weight residual 1.526 1.557 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 MAN A 5 " pdb=" C2 MAN A 5 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" N ASP L 1 " pdb=" H ASP L 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 6667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 11726 1.51 - 3.03: 178 3.03 - 4.54: 26 4.54 - 6.06: 7 6.06 - 7.57: 4 Bond angle restraints: 11941 Sorted by residual: angle pdb=" CA ARG L 97 " pdb=" CB ARG L 97 " pdb=" CG ARG L 97 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" N VAL H 102 " pdb=" CA VAL H 102 " pdb=" C VAL H 102 " ideal model delta sigma weight residual 110.21 106.93 3.28 1.13e+00 7.83e-01 8.43e+00 angle pdb=" C PRO L 96 " pdb=" N ARG L 97 " pdb=" CA ARG L 97 " ideal model delta sigma weight residual 122.30 125.62 -3.32 1.35e+00 5.49e-01 6.04e+00 angle pdb=" CB ARG L 97 " pdb=" CG ARG L 97 " pdb=" CD ARG L 97 " ideal model delta sigma weight residual 111.30 116.67 -5.37 2.30e+00 1.89e-01 5.45e+00 angle pdb=" C3 MAN A 4 " pdb=" C2 MAN A 4 " pdb=" O2 MAN A 4 " ideal model delta sigma weight residual 111.77 105.58 6.19 3.00e+00 1.11e-01 4.25e+00 ... (remaining 11936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 3063 21.62 - 43.23: 166 43.23 - 64.85: 57 64.85 - 86.47: 13 86.47 - 108.08: 5 Dihedral angle restraints: 3304 sinusoidal: 1796 harmonic: 1508 Sorted by residual: dihedral pdb=" CB CYS G 480 " pdb=" SG CYS G 480 " pdb=" SG CYS G 488 " pdb=" CB CYS G 488 " ideal model delta sinusoidal sigma weight residual 93.00 -178.36 -88.64 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 146.29 -53.29 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA PHE L 94 " pdb=" C PHE L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 454 0.054 - 0.107: 55 0.107 - 0.161: 25 0.161 - 0.214: 0 0.214 - 0.268: 1 Chirality restraints: 535 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C2 BMA A 3 " pdb=" C1 BMA A 3 " pdb=" C3 BMA A 3 " pdb=" O2 BMA A 3 " both_signs ideal model delta sigma weight residual False 2.47 2.61 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE G 402 " pdb=" N ILE G 402 " pdb=" C ILE G 402 " pdb=" CB ILE G 402 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 532 not shown) Planarity restraints: 1007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 97 " 0.199 9.50e-02 1.11e+02 6.65e-02 4.79e+00 pdb=" NE ARG L 97 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG L 97 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG L 97 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG L 97 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG L 97 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG L 97 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG L 97 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG L 97 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 520 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO G 521 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 521 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 521 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO L 96 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.015 5.00e-02 4.00e+02 ... (remaining 1004 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 288 2.17 - 2.78: 12644 2.78 - 3.38: 17363 3.38 - 3.99: 23147 3.99 - 4.60: 35239 Nonbonded interactions: 88681 Sorted by model distance: nonbonded pdb=" O TRP G 353 " pdb="HH12 ARG G 466 " model vdw 1.562 2.450 nonbonded pdb=" HG SER L 12 " pdb=" O ASP L 107 " model vdw 1.624 2.450 nonbonded pdb=" H LEU G 455 " pdb=" O PRO G 491 " model vdw 1.641 2.450 nonbonded pdb=" OE1 GLU L 81 " pdb=" H GLU L 81 " model vdw 1.643 2.450 nonbonded pdb=" OE1 GLU H 89 " pdb=" H GLU H 89 " model vdw 1.649 2.450 ... (remaining 88676 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: 0.420 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 0.033 3488 Z= 0.201 Angle : 0.609 7.571 4747 Z= 0.300 Chirality : 0.045 0.268 535 Planarity : 0.005 0.086 603 Dihedral : 15.740 108.084 1322 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.35 (0.42), residues: 421 helix: -1.99 (1.15), residues: 19 sheet: -0.82 (0.42), residues: 167 loop : -0.77 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS H 99 PHE 0.005 0.001 PHE G 400 TYR 0.011 0.001 TYR H 80 ARG 0.005 0.001 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 493 GLN cc_start: 0.8959 (tp-100) cc_final: 0.8639 (tp-100) REVERT: H 62 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8353 (tm-30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.3835 time to fit residues: 32.7141 Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 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 = 0.3020 r_free = 0.3020 target = 0.059043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.048725 restraints weight = 34397.940| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 4.29 r_work: 0.2621 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3488 Z= 0.293 Angle : 0.548 4.868 4747 Z= 0.291 Chirality : 0.042 0.170 535 Planarity : 0.004 0.029 603 Dihedral : 10.703 79.020 582 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.09 % Allowed : 8.74 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.52 (0.41), residues: 421 helix: -2.10 (1.11), residues: 20 sheet: -0.84 (0.43), residues: 155 loop : -0.97 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.003 0.001 HIS H 99 PHE 0.008 0.001 PHE H 64 TYR 0.010 0.001 TYR L 49 ARG 0.004 0.000 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8544 (tp-100) REVERT: H 62 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8606 (tm-30) REVERT: H 82 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7871 (tm-30) outliers start: 4 outliers final: 4 residues processed: 63 average time/residue: 0.3747 time to fit residues: 28.2870 Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** L 93 ASN ** 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 = 0.3002 r_free = 0.3002 target = 0.059223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.048282 restraints weight = 34635.174| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 4.31 r_work: 0.2581 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3488 Z= 0.353 Angle : 0.561 4.469 4747 Z= 0.292 Chirality : 0.043 0.172 535 Planarity : 0.004 0.032 603 Dihedral : 6.559 46.881 582 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 1.64 % Allowed : 7.65 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.68 (0.40), residues: 421 helix: -2.25 (1.06), residues: 20 sheet: -0.79 (0.43), residues: 152 loop : -1.20 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 436 HIS 0.004 0.002 HIS H 99 PHE 0.010 0.001 PHE H 64 TYR 0.025 0.001 TYR L 49 ARG 0.005 0.000 ARG G 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8593 (tp-100) REVERT: G 427 ASP cc_start: 0.8847 (m-30) cc_final: 0.8550 (p0) REVERT: H 62 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8671 (tm-30) REVERT: H 82 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7920 (tm-30) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.3791 time to fit residues: 28.5820 Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 0.0270 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 overall best weight: 1.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.059324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.048860 restraints weight = 33639.475| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 4.28 r_work: 0.2624 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3488 Z= 0.154 Angle : 0.507 5.302 4747 Z= 0.263 Chirality : 0.043 0.147 535 Planarity : 0.004 0.047 603 Dihedral : 5.907 46.993 582 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.64 % Allowed : 9.29 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.37 (0.41), residues: 421 helix: -1.91 (1.14), residues: 20 sheet: -0.55 (0.44), residues: 152 loop : -1.02 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 436 HIS 0.002 0.001 HIS L 90 PHE 0.007 0.001 PHE H 64 TYR 0.011 0.001 TYR L 49 ARG 0.004 0.000 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8515 (tp-100) REVERT: G 427 ASP cc_start: 0.8833 (m-30) cc_final: 0.8506 (p0) REVERT: H 62 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8636 (tm-30) REVERT: H 82 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7942 (tm-30) REVERT: L 27 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8387 (tp40) REVERT: L 55 GLU cc_start: 0.9464 (tp30) cc_final: 0.9169 (tp30) outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 0.3273 time to fit residues: 26.7265 Evaluate side-chains 65 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.058902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.048378 restraints weight = 33624.237| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 4.25 r_work: 0.2608 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3488 Z= 0.222 Angle : 0.508 4.975 4747 Z= 0.264 Chirality : 0.041 0.133 535 Planarity : 0.004 0.031 603 Dihedral : 5.772 46.529 582 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 1.37 % Allowed : 10.11 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.31 (0.41), residues: 421 helix: -2.00 (1.09), residues: 20 sheet: -0.53 (0.44), residues: 152 loop : -0.96 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.006 0.001 PHE H 64 TYR 0.030 0.001 TYR L 49 ARG 0.003 0.000 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8565 (tp-100) REVERT: G 427 ASP cc_start: 0.8812 (m-30) cc_final: 0.8525 (p0) REVERT: H 62 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8651 (tm-30) REVERT: H 82 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7998 (tm-30) REVERT: L 27 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8412 (tp40) outliers start: 5 outliers final: 5 residues processed: 61 average time/residue: 0.3362 time to fit residues: 25.4223 Evaluate side-chains 60 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 0.0370 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.060200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.049697 restraints weight = 33137.444| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 4.29 r_work: 0.2642 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3488 Z= 0.140 Angle : 0.495 5.392 4747 Z= 0.258 Chirality : 0.042 0.135 535 Planarity : 0.004 0.030 603 Dihedral : 5.466 46.553 582 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.37 % Allowed : 10.66 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.06 (0.42), residues: 421 helix: -1.74 (1.14), residues: 20 sheet: -0.37 (0.45), residues: 152 loop : -0.79 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.005 0.001 PHE G 400 TYR 0.017 0.001 TYR L 49 ARG 0.004 0.000 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 GLU cc_start: 0.9344 (tt0) cc_final: 0.8998 (tm-30) REVERT: G 427 ASP cc_start: 0.8812 (m-30) cc_final: 0.8499 (p0) REVERT: H 62 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8637 (tm-30) outliers start: 5 outliers final: 5 residues processed: 65 average time/residue: 0.2981 time to fit residues: 24.1702 Evaluate side-chains 66 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.060266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.049317 restraints weight = 34221.897| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 4.35 r_work: 0.2643 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3488 Z= 0.186 Angle : 0.507 5.096 4747 Z= 0.264 Chirality : 0.042 0.149 535 Planarity : 0.004 0.031 603 Dihedral : 5.338 46.426 582 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 1.37 % Allowed : 11.48 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.13 (0.42), residues: 421 helix: -1.75 (1.13), residues: 20 sheet: -0.47 (0.44), residues: 155 loop : -0.79 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 99 PHE 0.008 0.001 PHE H 64 TYR 0.031 0.001 TYR L 49 ARG 0.004 0.000 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 GLU cc_start: 0.9340 (tt0) cc_final: 0.9022 (tm-30) REVERT: G 414 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8489 (tp-100) REVERT: G 427 ASP cc_start: 0.8814 (m-30) cc_final: 0.8529 (p0) REVERT: H 62 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8605 (tm-30) REVERT: H 80 TYR cc_start: 0.8627 (m-80) cc_final: 0.8384 (m-80) outliers start: 5 outliers final: 5 residues processed: 62 average time/residue: 0.3037 time to fit residues: 23.4361 Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 0.0000 chunk 34 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 36 optimal weight: 0.3980 chunk 30 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.059433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.049200 restraints weight = 34179.268| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 4.23 r_work: 0.2627 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3488 Z= 0.198 Angle : 0.507 5.028 4747 Z= 0.265 Chirality : 0.042 0.136 535 Planarity : 0.004 0.035 603 Dihedral : 5.222 46.819 582 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.37 % Allowed : 11.48 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.07 (0.42), residues: 421 helix: -1.68 (1.15), residues: 20 sheet: -0.37 (0.45), residues: 152 loop : -0.81 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 99 PHE 0.005 0.001 PHE H 64 TYR 0.025 0.001 TYR L 49 ARG 0.004 0.000 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 GLU cc_start: 0.9352 (tt0) cc_final: 0.9047 (tm-30) REVERT: G 378 LYS cc_start: 0.9142 (ttmm) cc_final: 0.8646 (ptmm) REVERT: G 414 GLN cc_start: 0.8766 (tp-100) cc_final: 0.8461 (tp-100) REVERT: G 427 ASP cc_start: 0.8804 (m-30) cc_final: 0.8528 (p0) REVERT: H 62 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8597 (tm-30) outliers start: 5 outliers final: 5 residues processed: 61 average time/residue: 0.3049 time to fit residues: 23.2470 Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 38 optimal weight: 0.0060 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 overall best weight: 2.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 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 = 0.3032 r_free = 0.3032 target = 0.059522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.049143 restraints weight = 34497.331| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 4.30 r_work: 0.2629 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3488 Z= 0.190 Angle : 0.506 5.077 4747 Z= 0.265 Chirality : 0.041 0.137 535 Planarity : 0.004 0.037 603 Dihedral : 5.072 46.791 582 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 1.64 % Allowed : 12.57 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.05 (0.42), residues: 421 helix: -1.65 (1.16), residues: 20 sheet: -0.27 (0.45), residues: 151 loop : -0.85 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 99 PHE 0.011 0.001 PHE H 64 TYR 0.025 0.001 TYR L 49 ARG 0.005 0.000 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 GLU cc_start: 0.9360 (tt0) cc_final: 0.9059 (tm-30) REVERT: G 378 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8661 (ptmm) REVERT: G 414 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8444 (tp-100) REVERT: G 427 ASP cc_start: 0.8808 (m-30) cc_final: 0.8537 (p0) REVERT: H 62 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8616 (tm-30) REVERT: H 99 HIS cc_start: 0.9311 (OUTLIER) cc_final: 0.8563 (t-90) outliers start: 6 outliers final: 5 residues processed: 62 average time/residue: 0.2933 time to fit residues: 22.7753 Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 99 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 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 = 0.3021 r_free = 0.3021 target = 0.059101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.048866 restraints weight = 34343.804| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 4.25 r_work: 0.2617 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.003 0.024 3488 Z= 0.208 Angle : 0.515 5.013 4747 Z= 0.268 Chirality : 0.041 0.137 535 Planarity : 0.004 0.037 603 Dihedral : 5.046 46.794 582 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 1.64 % Allowed : 12.57 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.09 (0.42), residues: 421 helix: -1.66 (1.15), residues: 20 sheet: -0.31 (0.45), residues: 153 loop : -0.88 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 99 PHE 0.009 0.001 PHE H 64 TYR 0.023 0.001 TYR L 49 ARG 0.006 0.000 ARG H 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 GLU cc_start: 0.9355 (tt0) cc_final: 0.9095 (tm-30) REVERT: G 378 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8665 (ptmm) REVERT: G 414 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8441 (tp-100) REVERT: G 427 ASP cc_start: 0.8788 (m-30) cc_final: 0.8532 (p0) REVERT: H 62 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8614 (tm-30) REVERT: H 99 HIS cc_start: 0.9312 (OUTLIER) cc_final: 0.8528 (t-90) REVERT: L 38 GLN cc_start: 0.8679 (tp40) cc_final: 0.8457 (tp40) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.3111 time to fit residues: 23.6230 Evaluate side-chains 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 99 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.060175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.049676 restraints weight = 34412.445| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 4.35 r_work: 0.2641 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3488 Z= 0.151 Angle : 0.504 5.269 4747 Z= 0.263 Chirality : 0.042 0.175 535 Planarity : 0.004 0.037 603 Dihedral : 4.924 46.617 582 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.64 % Allowed : 12.84 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.99 (0.42), residues: 421 helix: -1.64 (1.15), residues: 20 sheet: -0.18 (0.45), residues: 151 loop : -0.84 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.010 0.001 PHE H 64 TYR 0.023 0.001 TYR L 49 ARG 0.005 0.000 ARG H 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3603.25 seconds wall clock time: 63 minutes 59.12 seconds (3839.12 seconds total)