Starting phenix.real_space_refine on Wed Jul 1 22:12:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dpz_27644/07_2026/8dpz_27644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpz_27644/07_2026/8dpz_27644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dpz_27644/07_2026/8dpz_27644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpz_27644/07_2026/8dpz_27644.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dpz_27644/07_2026/8dpz_27644.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dpz_27644/07_2026/8dpz_27644.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dpz_27644/07_2026/8dpz_27644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpz_27644/07_2026/8dpz_27644.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.017 sd= 0.107 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: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 2115 2.51 5 N 551 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3326 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1480 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain breaks: 1 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 982 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.98, per 1000 atoms: 0.29 Number of scatterers: 3326 At special positions: 0 Unit cell: (71.28, 90.72, 74.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 649 8.00 N 551 7.00 C 2115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 115.8 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 6 sheets defined 11.2% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.210A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.822A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.608A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.959A pdb=" N THR F 87 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.535A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N GLU F 100H" --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 12.269A pdb=" N TYR F 98 " --> pdb=" O GLU F 100H" (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA F 100J" --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.535A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N GLU F 100H" --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 12.269A pdb=" N TYR F 98 " --> pdb=" O GLU F 100H" (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA F 100J" --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN F 33 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.623A pdb=" N GLN F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.536A pdb=" N ALA G 34 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR G 49 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.47 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1045 1.34 - 1.46: 898 1.46 - 1.58: 1458 1.58 - 1.70: 0 1.70 - 1.81: 12 Bond restraints: 3413 Sorted by residual: bond pdb=" C GLU G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.334 1.351 -0.018 8.40e-03 1.42e+04 4.43e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C SER G 7 " pdb=" N PRO G 8 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.27e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 bond pdb=" CB ASP F 100A" pdb=" CG ASP F 100A" ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.70e+00 ... (remaining 3408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 4413 1.63 - 3.26: 188 3.26 - 4.89: 31 4.89 - 6.51: 7 6.51 - 8.14: 3 Bond angle restraints: 4642 Sorted by residual: angle pdb=" C ASP G 50 " pdb=" N ALA G 51 " pdb=" CA ALA G 51 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.29e+00 angle pdb=" N ASP F 100 " pdb=" CA ASP F 100 " pdb=" C ASP F 100 " ideal model delta sigma weight residual 109.95 105.91 4.04 1.44e+00 4.82e-01 7.86e+00 angle pdb=" C ASN G 93 " pdb=" N TRP G 94 " pdb=" CA TRP G 94 " ideal model delta sigma weight residual 120.06 123.39 -3.33 1.19e+00 7.06e-01 7.81e+00 angle pdb=" C PHE G 83 " pdb=" CA PHE G 83 " pdb=" CB PHE G 83 " ideal model delta sigma weight residual 111.31 115.81 -4.50 1.68e+00 3.54e-01 7.18e+00 angle pdb=" N TRP G 94 " pdb=" CA TRP G 94 " pdb=" C TRP G 94 " ideal model delta sigma weight residual 113.57 117.12 -3.55 1.38e+00 5.25e-01 6.62e+00 ... (remaining 4637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 1783 16.50 - 33.01: 174 33.01 - 49.51: 25 49.51 - 66.02: 5 66.02 - 82.52: 4 Dihedral angle restraints: 1991 sinusoidal: 775 harmonic: 1216 Sorted by residual: dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.65 36.35 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA VAL F 95 " pdb=" C VAL F 95 " pdb=" N ALA F 96 " pdb=" CA ALA F 96 " ideal model delta harmonic sigma weight residual 180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASN G 93 " pdb=" C ASN G 93 " pdb=" N TRP G 94 " pdb=" CA TRP G 94 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 1988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 290 0.035 - 0.070: 137 0.070 - 0.106: 51 0.106 - 0.141: 19 0.141 - 0.176: 4 Chirality restraints: 501 Sorted by residual: chirality pdb=" CB THR G 102 " pdb=" CA THR G 102 " pdb=" OG1 THR G 102 " pdb=" CG2 THR G 102 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA TRP G 94 " pdb=" N TRP G 94 " pdb=" C TRP G 94 " pdb=" CB TRP G 94 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ILE B 402 " pdb=" N ILE B 402 " pdb=" C ILE B 402 " pdb=" CB ILE B 402 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 498 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 79 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO G 80 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO B 337 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 83 " -0.014 2.00e-02 2.50e+03 1.57e-02 4.33e+00 pdb=" CG PHE G 83 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE G 83 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 83 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE G 83 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 83 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE G 83 " -0.001 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1186 2.87 - 3.38: 2663 3.38 - 3.89: 5282 3.89 - 4.39: 5920 4.39 - 4.90: 10828 Nonbonded interactions: 25879 Sorted by model distance: nonbonded pdb=" OH TYR F 97 " pdb=" OE1 GLU F 99 " model vdw 2.363 3.040 nonbonded pdb=" OD2 ASP B 405 " pdb=" OG SER G 30 " model vdw 2.408 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.420 3.120 nonbonded pdb=" OD1 ASP F 100 " pdb=" N ASP F 100A" model vdw 2.427 3.120 nonbonded pdb=" NH1 ARG G 61 " pdb=" OD2 ASP G 82 " model vdw 2.429 3.120 ... (remaining 25874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.004 0.042 3420 Z= 0.188 Angle : 0.774 8.142 4658 Z= 0.412 Chirality : 0.050 0.176 501 Planarity : 0.007 0.069 595 Dihedral : 13.132 82.522 1206 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.38), residues: 412 helix: -4.20 (0.35), residues: 27 sheet: -0.08 (0.45), residues: 139 loop : -1.92 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 24 TYR 0.018 0.002 TYR G 49 PHE 0.037 0.003 PHE G 83 TRP 0.012 0.002 TRP F 103 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 ( 3413) covalent geometry : angle 0.77180 / 0.41 ( 4642) SS BOND : bond 0.00146 / 0.09 ( 5) SS BOND : angle 0.64337 / 0.35 ( 10) hydrogen bonds : bond 0.24268 / 15.78 ( 104) hydrogen bonds : angle 10.69454 / 7.43 ( 324) link_BETA1-4 : bond 0.00751 / 0.40 ( 1) link_BETA1-4 : angle 1.33408 / 0.62 ( 3) link_NAG-ASN : bond 0.00387 / 0.20 ( 1) link_NAG-ASN : angle 2.27697 / 1.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.134 Fit side-chains REVERT: B 406 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7917 (mt-10) REVERT: B 417 LYS cc_start: 0.8402 (tppt) cc_final: 0.8168 (tptt) REVERT: F 48 ILE cc_start: 0.8306 (mm) cc_final: 0.7983 (mm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0915 time to fit residues: 7.0019 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099600 restraints weight = 5126.395| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.29 r_work: 0.3165 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3420 Z= 0.148 Angle : 0.583 5.809 4658 Z= 0.308 Chirality : 0.045 0.153 501 Planarity : 0.005 0.052 595 Dihedral : 5.011 18.118 468 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.40), residues: 412 helix: -3.75 (0.52), residues: 28 sheet: 0.30 (0.47), residues: 140 loop : -1.60 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.011 0.001 TYR F 100F PHE 0.021 0.002 PHE G 83 TRP 0.012 0.002 TRP G 94 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 3413) covalent geometry : angle 0.57463 / 0.31 ( 4642) SS BOND : bond 0.00573 / 0.25 ( 5) SS BOND : angle 1.94053 / 1.14 ( 10) hydrogen bonds : bond 0.04190 / 2.75 ( 104) hydrogen bonds : angle 6.65525 / 4.59 ( 324) link_BETA1-4 : bond 0.00258 / 0.14 ( 1) link_BETA1-4 : angle 1.08751 / 0.54 ( 3) link_NAG-ASN : bond 0.00087 / 0.05 ( 1) link_NAG-ASN : angle 1.50422 / 0.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.125 Fit side-chains REVERT: B 406 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8461 (mt-10) REVERT: B 417 LYS cc_start: 0.8598 (tppt) cc_final: 0.8298 (tptt) REVERT: F 48 ILE cc_start: 0.8517 (mm) cc_final: 0.8287 (mm) REVERT: F 100 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7732 (tm-30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1008 time to fit residues: 7.1101 Evaluate side-chains 56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098590 restraints weight = 5142.172| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.19 r_work: 0.3156 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 3420 Z= 0.174 Angle : 0.618 11.204 4658 Z= 0.321 Chirality : 0.047 0.164 501 Planarity : 0.005 0.047 595 Dihedral : 5.026 20.677 468 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.94 % Allowed : 7.50 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.40), residues: 412 helix: -3.30 (0.68), residues: 28 sheet: 0.20 (0.45), residues: 148 loop : -1.47 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.014 0.001 TYR F 100F PHE 0.020 0.002 PHE G 83 TRP 0.013 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 3413) covalent geometry : angle 0.61289 / 0.32 ( 4642) SS BOND : bond 0.01059 / 0.41 ( 5) SS BOND : angle 1.69097 / 0.78 ( 10) hydrogen bonds : bond 0.03877 / 2.52 ( 104) hydrogen bonds : angle 5.98200 / 4.12 ( 324) link_BETA1-4 : bond 0.00410 / 0.22 ( 1) link_BETA1-4 : angle 1.04095 / 0.53 ( 3) link_NAG-ASN : bond 0.00088 / 0.05 ( 1) link_NAG-ASN : angle 1.41990 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.151 Fit side-chains REVERT: B 403 ARG cc_start: 0.8260 (mtp-110) cc_final: 0.7980 (mtp85) REVERT: B 417 LYS cc_start: 0.8616 (tppt) cc_final: 0.8263 (tppt) REVERT: F 48 ILE cc_start: 0.8555 (mm) cc_final: 0.8329 (mm) REVERT: F 100 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7737 (tm-30) outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 0.1090 time to fit residues: 7.6963 Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097796 restraints weight = 5098.778| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.33 r_work: 0.3144 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3420 Z= 0.163 Angle : 0.597 10.155 4658 Z= 0.312 Chirality : 0.046 0.169 501 Planarity : 0.004 0.044 595 Dihedral : 4.992 21.332 468 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.22 % Allowed : 10.00 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.40), residues: 412 helix: -3.08 (0.76), residues: 28 sheet: 0.20 (0.45), residues: 147 loop : -1.45 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 18 TYR 0.011 0.001 TYR B 453 PHE 0.019 0.002 PHE G 83 TRP 0.012 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 3413) covalent geometry : angle 0.59321 / 0.31 ( 4642) SS BOND : bond 0.00774 / 0.31 ( 5) SS BOND : angle 1.36872 / 0.73 ( 10) hydrogen bonds : bond 0.03577 / 2.32 ( 104) hydrogen bonds : angle 5.66101 / 3.86 ( 324) link_BETA1-4 : bond 0.00275 / 0.14 ( 1) link_BETA1-4 : angle 0.97891 / 0.50 ( 3) link_NAG-ASN : bond 0.00133 / 0.07 ( 1) link_NAG-ASN : angle 1.40317 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.121 Fit side-chains REVERT: B 347 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7659 (m-10) REVERT: B 417 LYS cc_start: 0.8617 (tppt) cc_final: 0.8271 (tptt) REVERT: F 100 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7647 (tm-30) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 0.0685 time to fit residues: 4.8012 Evaluate side-chains 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098649 restraints weight = 5118.428| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.41 r_work: 0.3150 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3420 Z= 0.134 Angle : 0.584 8.936 4658 Z= 0.299 Chirality : 0.046 0.161 501 Planarity : 0.004 0.044 595 Dihedral : 4.850 20.581 468 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.06 % Allowed : 11.39 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.40), residues: 412 helix: -2.10 (1.29), residues: 15 sheet: 0.16 (0.45), residues: 149 loop : -1.50 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 18 TYR 0.015 0.001 TYR F 100F PHE 0.016 0.002 PHE G 83 TRP 0.011 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 3413) covalent geometry : angle 0.58017 / 0.30 ( 4642) SS BOND : bond 0.00676 / 0.28 ( 5) SS BOND : angle 1.30706 / 0.74 ( 10) hydrogen bonds : bond 0.03385 / 2.21 ( 104) hydrogen bonds : angle 5.46927 / 3.71 ( 324) link_BETA1-4 : bond 0.00273 / 0.14 ( 1) link_BETA1-4 : angle 0.93233 / 0.48 ( 3) link_NAG-ASN : bond 0.00083 / 0.04 ( 1) link_NAG-ASN : angle 1.36504 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.127 Fit side-chains REVERT: B 347 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.7557 (m-10) REVERT: B 376 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8706 (p) REVERT: B 417 LYS cc_start: 0.8559 (tppt) cc_final: 0.8131 (tppt) REVERT: B 418 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7583 (mt) REVERT: F 82 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7732 (mp) REVERT: F 100 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7600 (tm-30) outliers start: 11 outliers final: 3 residues processed: 63 average time/residue: 0.0808 time to fit residues: 6.1084 Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099533 restraints weight = 5115.844| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.24 r_work: 0.3168 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3420 Z= 0.141 Angle : 0.585 8.610 4658 Z= 0.301 Chirality : 0.045 0.158 501 Planarity : 0.004 0.043 595 Dihedral : 4.799 20.179 468 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.33 % Allowed : 10.56 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.39), residues: 412 helix: -2.62 (0.97), residues: 21 sheet: -0.03 (0.46), residues: 137 loop : -1.45 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 18 TYR 0.014 0.001 TYR F 100F PHE 0.017 0.002 PHE G 83 TRP 0.011 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 3413) covalent geometry : angle 0.58172 / 0.30 ( 4642) SS BOND : bond 0.00666 / 0.27 ( 5) SS BOND : angle 1.31410 / 0.76 ( 10) hydrogen bonds : bond 0.03343 / 2.17 ( 104) hydrogen bonds : angle 5.42943 / 3.67 ( 324) link_BETA1-4 : bond 0.00278 / 0.15 ( 1) link_BETA1-4 : angle 0.94195 / 0.49 ( 3) link_NAG-ASN : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : angle 1.39126 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.129 Fit side-chains REVERT: B 347 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7702 (m-10) REVERT: B 376 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8754 (p) REVERT: B 417 LYS cc_start: 0.8635 (tppt) cc_final: 0.8220 (tppt) REVERT: B 418 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7753 (mt) REVERT: F 82 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7874 (mp) REVERT: F 100 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7663 (tm-30) outliers start: 12 outliers final: 5 residues processed: 62 average time/residue: 0.0814 time to fit residues: 6.0857 Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098603 restraints weight = 5215.213| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.29 r_work: 0.3148 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3420 Z= 0.162 Angle : 0.609 8.763 4658 Z= 0.313 Chirality : 0.046 0.178 501 Planarity : 0.004 0.041 595 Dihedral : 4.874 20.513 468 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.06 % Allowed : 12.22 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.40), residues: 412 helix: -2.83 (0.80), residues: 28 sheet: 0.04 (0.47), residues: 135 loop : -1.38 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.017 0.001 TYR F 100F PHE 0.018 0.002 PHE G 83 TRP 0.011 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 3413) covalent geometry : angle 0.60523 / 0.31 ( 4642) SS BOND : bond 0.00732 / 0.30 ( 5) SS BOND : angle 1.36979 / 0.78 ( 10) hydrogen bonds : bond 0.03433 / 2.25 ( 104) hydrogen bonds : angle 5.45824 / 3.68 ( 324) link_BETA1-4 : bond 0.00272 / 0.14 ( 1) link_BETA1-4 : angle 0.97040 / 0.50 ( 3) link_NAG-ASN : bond 0.00157 / 0.08 ( 1) link_NAG-ASN : angle 1.46685 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.127 Fit side-chains REVERT: B 347 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7750 (m-10) REVERT: B 376 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8727 (p) REVERT: B 417 LYS cc_start: 0.8632 (tppt) cc_final: 0.8317 (tptt) REVERT: F 82 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7845 (mp) REVERT: F 100 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7713 (tm-30) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.0712 time to fit residues: 5.0327 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098272 restraints weight = 5217.553| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.28 r_work: 0.3144 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3420 Z= 0.173 Angle : 0.615 8.797 4658 Z= 0.317 Chirality : 0.046 0.170 501 Planarity : 0.004 0.041 595 Dihedral : 4.941 20.467 468 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.33 % Allowed : 12.50 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.40), residues: 412 helix: -2.90 (0.78), residues: 28 sheet: 0.03 (0.48), residues: 135 loop : -1.44 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.018 0.001 TYR F 100F PHE 0.018 0.002 PHE G 83 TRP 0.010 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 3413) covalent geometry : angle 0.61091 / 0.32 ( 4642) SS BOND : bond 0.00749 / 0.30 ( 5) SS BOND : angle 1.42414 / 0.82 ( 10) hydrogen bonds : bond 0.03404 / 2.20 ( 104) hydrogen bonds : angle 5.48604 / 3.70 ( 324) link_BETA1-4 : bond 0.00256 / 0.13 ( 1) link_BETA1-4 : angle 0.97151 / 0.50 ( 3) link_NAG-ASN : bond 0.00189 / 0.10 ( 1) link_NAG-ASN : angle 1.50017 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.126 Fit side-chains REVERT: B 347 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.7744 (m-10) REVERT: B 376 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8719 (p) REVERT: B 417 LYS cc_start: 0.8629 (tppt) cc_final: 0.8315 (tptt) REVERT: B 418 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7962 (mt) REVERT: F 82 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7852 (mp) REVERT: F 100 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7736 (tm-30) outliers start: 12 outliers final: 6 residues processed: 62 average time/residue: 0.0874 time to fit residues: 6.4417 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 0.0000 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100420 restraints weight = 5123.507| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.27 r_work: 0.3175 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3420 Z= 0.123 Angle : 0.580 7.868 4658 Z= 0.298 Chirality : 0.045 0.150 501 Planarity : 0.004 0.041 595 Dihedral : 4.695 19.123 468 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.22 % Allowed : 14.72 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.40), residues: 412 helix: -2.71 (0.92), residues: 22 sheet: 0.06 (0.48), residues: 137 loop : -1.33 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 50 TYR 0.014 0.001 TYR F 100F PHE 0.015 0.002 PHE G 83 TRP 0.012 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 3413) covalent geometry : angle 0.57671 / 0.30 ( 4642) SS BOND : bond 0.00723 / 0.30 ( 5) SS BOND : angle 1.35126 / 0.79 ( 10) hydrogen bonds : bond 0.03087 / 2.02 ( 104) hydrogen bonds : angle 5.35895 / 3.61 ( 324) link_BETA1-4 : bond 0.00271 / 0.14 ( 1) link_BETA1-4 : angle 0.89420 / 0.46 ( 3) link_NAG-ASN : bond 0.00054 / 0.03 ( 1) link_NAG-ASN : angle 1.29137 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.127 Fit side-chains REVERT: B 347 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7537 (m-10) REVERT: B 376 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8720 (p) REVERT: B 417 LYS cc_start: 0.8615 (tppt) cc_final: 0.8172 (tppt) REVERT: B 418 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7862 (mt) REVERT: F 82 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7831 (mp) REVERT: F 100 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7621 (tm-30) outliers start: 8 outliers final: 3 residues processed: 59 average time/residue: 0.0904 time to fit residues: 6.3022 Evaluate side-chains 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 0.0670 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.101274 restraints weight = 5123.809| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.19 r_work: 0.3191 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3420 Z= 0.119 Angle : 0.576 7.683 4658 Z= 0.294 Chirality : 0.044 0.146 501 Planarity : 0.004 0.041 595 Dihedral : 4.609 18.518 468 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.22 % Allowed : 15.56 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.40), residues: 412 helix: -2.52 (0.94), residues: 22 sheet: 0.07 (0.48), residues: 137 loop : -1.22 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 18 TYR 0.014 0.001 TYR F 100F PHE 0.015 0.001 PHE G 83 TRP 0.012 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 3413) covalent geometry : angle 0.57258 / 0.29 ( 4642) SS BOND : bond 0.00702 / 0.30 ( 5) SS BOND : angle 1.31213 / 0.77 ( 10) hydrogen bonds : bond 0.03029 / 1.98 ( 104) hydrogen bonds : angle 5.27250 / 3.57 ( 324) link_BETA1-4 : bond 0.00288 / 0.15 ( 1) link_BETA1-4 : angle 0.88460 / 0.46 ( 3) link_NAG-ASN : bond 0.00051 / 0.03 ( 1) link_NAG-ASN : angle 1.25070 / 0.70 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.124 Fit side-chains REVERT: B 347 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: B 376 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8708 (p) REVERT: B 417 LYS cc_start: 0.8634 (tppt) cc_final: 0.8203 (tppt) REVERT: B 418 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7888 (mt) REVERT: F 82 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7838 (mp) REVERT: F 99 GLU cc_start: 0.8775 (tt0) cc_final: 0.8555 (tt0) REVERT: F 100 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7653 (tm-30) outliers start: 8 outliers final: 3 residues processed: 59 average time/residue: 0.0944 time to fit residues: 6.6139 Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.101086 restraints weight = 5169.154| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.29 r_work: 0.3186 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3420 Z= 0.119 Angle : 0.575 7.618 4658 Z= 0.293 Chirality : 0.044 0.145 501 Planarity : 0.004 0.041 595 Dihedral : 4.584 18.315 468 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.78 % Allowed : 15.00 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.40), residues: 412 helix: -2.46 (0.96), residues: 22 sheet: 0.09 (0.48), residues: 137 loop : -1.19 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 18 TYR 0.014 0.001 TYR F 100F PHE 0.015 0.001 PHE G 83 TRP 0.011 0.001 TRP G 94 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 3413) covalent geometry : angle 0.57102 / 0.29 ( 4642) SS BOND : bond 0.00691 / 0.29 ( 5) SS BOND : angle 1.32887 / 0.77 ( 10) hydrogen bonds : bond 0.03005 / 1.96 ( 104) hydrogen bonds : angle 5.23964 / 3.54 ( 324) link_BETA1-4 : bond 0.00300 / 0.16 ( 1) link_BETA1-4 : angle 0.88003 / 0.46 ( 3) link_NAG-ASN : bond 0.00032 / 0.02 ( 1) link_NAG-ASN : angle 1.22795 / 0.69 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1153.60 seconds wall clock time: 20 minutes 27.46 seconds (1227.46 seconds total)