Starting phenix.real_space_refine on Tue Mar 11 21:54:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x96_33068/03_2025/7x96_33068_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x96_33068/03_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_33068/03_2025/7x96_33068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x96_33068/03_2025/7x96_33068.map" model { file = "/net/cci-nas-00/data/ceres_data/7x96_33068/03_2025/7x96_33068_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x96_33068/03_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-5624/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: 3.90, per 1000 atoms: 0.59 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: 1.96 Conformation dependent library (CDL) restraints added in 599.9 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: 0.94 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: 2.31 Time building geometry restraints manager: 2.34 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.760 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- 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 : 0.519 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: 0.3731 time to fit residues: 31.9204 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 : 0.503 ------------------------------------------------------------------------------- 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: 8.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3004 r_free = 0.3004 target = 0.058591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.048243 restraints weight = 34464.015| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 4.29 r_work: 0.2609 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3488 Z= 0.305 Angle : 0.553 4.811 4747 Z= 0.293 Chirality : 0.042 0.174 535 Planarity : 0.004 0.032 603 Dihedral : 10.293 75.302 582 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 1.09 % Allowed : 8.47 % Favored : 90.44 % 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: -1.47 (0.41), residues: 421 helix: -2.05 (1.13), residues: 20 sheet: -0.77 (0.43), residues: 152 loop : -0.97 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 47 HIS 0.004 0.001 HIS H 99 PHE 0.009 0.001 PHE H 64 TYR 0.011 0.001 TYR L 49 ARG 0.003 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 : 0.516 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: 0.8811 (tp-100) cc_final: 0.8538 (tp-100) REVERT: H 62 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8617 (tm-30) REVERT: H 82 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7867 (tm-30) outliers start: 4 outliers final: 4 residues processed: 63 average time/residue: 0.3687 time to fit residues: 27.8508 Evaluate side-chains 63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.059330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.048954 restraints weight = 33820.443| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 4.27 r_work: 0.2626 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1463 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= 0.198 Angle : 0.525 5.028 4747 Z= 0.270 Chirality : 0.043 0.202 535 Planarity : 0.004 0.040 603 Dihedral : 6.486 48.338 582 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 1.09 % Allowed : 7.92 % Favored : 90.98 % 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: -1.42 (0.41), residues: 421 helix: -1.98 (1.12), residues: 20 sheet: -0.59 (0.44), residues: 152 loop : -1.05 (0.39), residues: 249 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 0.006 0.001 TYR G 380 ARG 0.003 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: 4 poor density : 64 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: symmetry clash REVERT: G 414 GLN cc_start: 0.8850 (tp-100) cc_final: 0.8539 (tp-100) REVERT: G 427 ASP cc_start: 0.8837 (m-30) cc_final: 0.8518 (p0) REVERT: H 62 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8610 (tm-30) REVERT: H 82 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7869 (tm-30) REVERT: L 42 GLN cc_start: 0.8336 (mp10) cc_final: 0.8033 (mp10) outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 0.3613 time to fit residues: 28.0615 Evaluate side-chains 63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.059436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.049116 restraints weight = 33620.723| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 4.25 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: 0.8257 moved from start: 0.1633 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= 0.178 Angle : 0.501 5.098 4747 Z= 0.259 Chirality : 0.042 0.143 535 Planarity : 0.004 0.046 603 Dihedral : 5.849 46.770 582 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.09 % Allowed : 9.56 % Favored : 89.34 % 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: -1.26 (0.42), residues: 421 helix: -1.85 (1.14), residues: 20 sheet: -0.49 (0.44), residues: 152 loop : -0.94 (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 H 99 PHE 0.007 0.001 PHE H 64 TYR 0.026 0.001 TYR L 49 ARG 0.005 0.001 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 69 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8537 (tp-100) REVERT: G 427 ASP cc_start: 0.8830 (m-30) cc_final: 0.8504 (p0) REVERT: H 62 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8623 (tm-30) REVERT: H 82 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7962 (tm-30) REVERT: L 27 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8396 (tp40) REVERT: L 42 GLN cc_start: 0.8380 (mp10) cc_final: 0.8156 (mp10) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 0.4063 time to fit residues: 31.8479 Evaluate side-chains 63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3022 r_free = 0.3022 target = 0.059324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.048862 restraints weight = 33518.152| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 4.30 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: 0.8265 moved from start: 0.1720 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= 0.185 Angle : 0.499 5.063 4747 Z= 0.259 Chirality : 0.042 0.134 535 Planarity : 0.004 0.048 603 Dihedral : 5.685 46.900 582 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.37 % Allowed : 9.84 % Favored : 88.80 % 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: -1.19 (0.41), residues: 421 helix: -1.83 (1.11), residues: 20 sheet: -0.43 (0.44), residues: 152 loop : -0.90 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 436 HIS 0.002 0.001 HIS H 99 PHE 0.007 0.001 PHE H 64 TYR 0.024 0.001 TYR L 49 ARG 0.006 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 67 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 GLU cc_start: 0.9347 (tt0) cc_final: 0.9010 (tm-30) REVERT: G 427 ASP cc_start: 0.8834 (m-30) cc_final: 0.8533 (p0) REVERT: H 62 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8646 (tm-30) REVERT: L 27 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8399 (tp40) REVERT: L 42 GLN cc_start: 0.8405 (mp10) cc_final: 0.8179 (mp10) REVERT: L 102 GLN cc_start: 0.9531 (mm-40) cc_final: 0.9300 (mm-40) outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 0.3716 time to fit residues: 28.4761 Evaluate side-chains 63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.3018 r_free = 0.3018 target = 0.059222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.048827 restraints weight = 33633.686| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 4.28 r_work: 0.2619 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1882 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= 0.206 Angle : 0.499 5.004 4747 Z= 0.261 Chirality : 0.041 0.135 535 Planarity : 0.004 0.029 603 Dihedral : 5.477 46.886 582 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.64 % Allowed : 10.93 % Favored : 87.43 % 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: -1.21 (0.42), residues: 421 helix: -1.73 (1.15), residues: 20 sheet: -0.54 (0.44), residues: 155 loop : -0.85 (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 0.007 0.001 PHE H 64 TYR 0.027 0.001 TYR L 49 ARG 0.004 0.001 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 67 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 GLU cc_start: 0.9346 (tt0) cc_final: 0.9020 (tm-30) REVERT: G 414 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8467 (tp-100) REVERT: G 427 ASP cc_start: 0.8822 (m-30) cc_final: 0.8519 (p0) REVERT: H 62 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8649 (tm-30) REVERT: L 27 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8401 (tp40) REVERT: L 42 GLN cc_start: 0.8403 (mp10) cc_final: 0.8173 (mp10) REVERT: L 102 GLN cc_start: 0.9531 (mm-40) cc_final: 0.9309 (mm-40) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.3791 time to fit residues: 28.6405 Evaluate side-chains 63 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 96 CYS Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 0.0370 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.7462 ------------------------------------------------------------------------------- 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 = 0.3029 r_free = 0.3029 target = 0.059746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.049272 restraints weight = 33267.386| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 4.30 r_work: 0.2629 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1900 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= 0.164 Angle : 0.496 5.199 4747 Z= 0.257 Chirality : 0.042 0.173 535 Planarity : 0.004 0.032 603 Dihedral : 5.297 46.867 582 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.37 % Allowed : 10.93 % Favored : 87.70 % 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: -1.12 (0.42), residues: 421 helix: -1.66 (1.15), residues: 20 sheet: -0.34 (0.45), residues: 151 loop : -0.89 (0.40), residues: 250 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 0.007 0.001 PHE H 64 TYR 0.026 0.001 TYR L 49 ARG 0.005 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 64 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.502 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: 0.9342 (tt0) cc_final: 0.9021 (tm-30) REVERT: G 378 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8610 (ptmm) REVERT: G 414 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8431 (tp-100) REVERT: G 427 ASP cc_start: 0.8818 (m-30) cc_final: 0.8523 (p0) REVERT: H 62 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8625 (tm-30) REVERT: L 42 GLN cc_start: 0.8380 (mp10) cc_final: 0.8147 (mp10) REVERT: L 102 GLN cc_start: 0.9539 (mm-40) cc_final: 0.9320 (mm-40) outliers start: 5 outliers final: 5 residues processed: 61 average time/residue: 0.3466 time to fit residues: 25.5121 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 : 0.504 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3027 r_free = 0.3027 target = 0.059599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.049178 restraints weight = 33606.891| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 4.30 r_work: 0.2625 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3488 Z= 0.183 Angle : 0.493 5.103 4747 Z= 0.257 Chirality : 0.041 0.136 535 Planarity : 0.004 0.035 603 Dihedral : 5.149 46.781 582 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.64 % Allowed : 12.02 % Favored : 86.34 % 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: -1.11 (0.42), residues: 421 helix: -1.64 (1.16), residues: 20 sheet: -0.34 (0.45), residues: 151 loop : -0.88 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.002 0.001 HIS H 99 PHE 0.010 0.001 PHE H 64 TYR 0.024 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 65 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.557 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: 0.9361 (tt0) cc_final: 0.9045 (tm-30) REVERT: G 378 LYS cc_start: 0.9127 (ttmm) cc_final: 0.8631 (ptmm) REVERT: G 414 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8448 (tp-100) REVERT: G 427 ASP cc_start: 0.8810 (m-30) cc_final: 0.8526 (p0) REVERT: H 62 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8622 (tm-30) REVERT: L 42 GLN cc_start: 0.8423 (mp10) cc_final: 0.8193 (mp10) REVERT: L 102 GLN cc_start: 0.9543 (mm-40) cc_final: 0.9325 (mm-40) outliers start: 6 outliers final: 6 residues processed: 61 average time/residue: 0.3538 time to fit residues: 26.0892 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 : 0.578 ------------------------------------------------------------------------------- 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 L residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 0.0020 chunk 16 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 = 0.3049 r_free = 0.3049 target = 0.061270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.050373 restraints weight = 33835.099| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 4.43 r_work: 0.2651 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3488 Z= 0.137 Angle : 0.489 5.392 4747 Z= 0.255 Chirality : 0.042 0.137 535 Planarity : 0.004 0.037 603 Dihedral : 4.923 46.269 582 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.37 % Allowed : 12.57 % Favored : 86.07 % 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: -1.07 (0.42), residues: 421 helix: -1.58 (1.17), residues: 20 sheet: -0.42 (0.44), residues: 155 loop : -0.77 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.008 0.001 PHE H 64 TYR 0.024 0.001 TYR L 49 ARG 0.006 0.001 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 69 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 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: symmetry clash REVERT: G 340 GLU cc_start: 0.9337 (tt0) cc_final: 0.9067 (tm-30) REVERT: G 378 LYS cc_start: 0.9174 (ttmm) cc_final: 0.8697 (ptmm) REVERT: G 414 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8453 (tp-100) REVERT: G 427 ASP cc_start: 0.8818 (m-30) cc_final: 0.8507 (p0) REVERT: H 62 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8608 (tm-30) REVERT: L 42 GLN cc_start: 0.8384 (mp10) cc_final: 0.8151 (mp10) REVERT: L 102 GLN cc_start: 0.9532 (mm-40) cc_final: 0.9320 (mm-40) REVERT: L 107 ASP cc_start: 0.8364 (t70) cc_final: 0.8002 (p0) outliers start: 5 outliers final: 5 residues processed: 66 average time/residue: 0.3342 time to fit residues: 26.7591 Evaluate side-chains 67 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3036 r_free = 0.3036 target = 0.059997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.049587 restraints weight = 33568.181| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 4.31 r_work: 0.2640 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2128 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= 0.172 Angle : 0.490 5.105 4747 Z= 0.255 Chirality : 0.041 0.135 535 Planarity : 0.004 0.036 603 Dihedral : 4.869 46.468 582 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.64 % Allowed : 11.75 % Favored : 86.61 % 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: -1.11 (0.42), residues: 421 helix: -1.61 (1.15), residues: 20 sheet: -0.42 (0.44), residues: 156 loop : -0.82 (0.40), residues: 245 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 0.007 0.001 PHE H 64 TYR 0.022 0.001 TYR L 49 ARG 0.005 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 67 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.588 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: 0.9348 (tt0) cc_final: 0.9086 (tm-30) REVERT: G 378 LYS cc_start: 0.9154 (ttmm) cc_final: 0.8673 (ptmm) REVERT: G 414 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8430 (tp-100) REVERT: G 427 ASP cc_start: 0.8808 (m-30) cc_final: 0.8530 (p0) REVERT: H 62 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8621 (tm-30) REVERT: H 99 HIS cc_start: 0.9289 (OUTLIER) cc_final: 0.8576 (t-90) REVERT: L 42 GLN cc_start: 0.8416 (mp10) cc_final: 0.8171 (mp10) REVERT: L 102 GLN cc_start: 0.9536 (mm-40) cc_final: 0.9322 (mm-40) REVERT: L 107 ASP cc_start: 0.8359 (t70) cc_final: 0.7937 (p0) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.3522 time to fit residues: 27.3494 Evaluate side-chains 66 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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: 6.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3038 r_free = 0.3038 target = 0.060283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.049708 restraints weight = 33640.844| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 4.36 r_work: 0.2639 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3488 Z= 0.152 Angle : 0.493 5.198 4747 Z= 0.258 Chirality : 0.042 0.143 535 Planarity : 0.004 0.037 603 Dihedral : 4.805 46.593 582 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.64 % Allowed : 12.02 % Favored : 86.34 % 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: -1.60 (1.16), residues: 20 sheet: -0.36 (0.44), residues: 156 loop : -0.80 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.008 0.001 PHE H 64 TYR 0.024 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: 3612.32 seconds wall clock time: 62 minutes 9.35 seconds (3729.35 seconds total)