Starting phenix.real_space_refine on Tue Mar 3 15:01:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7phg_13415/03_2026/7phg_13415_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7phg_13415/03_2026/7phg_13415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7phg_13415/03_2026/7phg_13415_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7phg_13415/03_2026/7phg_13415_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7phg_13415/03_2026/7phg_13415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7phg_13415/03_2026/7phg_13415.map" } resolution = 4.3 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= -0.000 sd= 1.000 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 18 5.16 5 C 2093 2.51 5 N 558 2.21 5 O 640 1.98 5 H 3160 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6469 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3022 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1819 Classifications: {'peptide': 123} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1628 Classifications: {'peptide': 108} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Time building chain proxies: 1.01, per 1000 atoms: 0.16 Number of scatterers: 6469 At special positions: 0 Unit cell: (72.98, 52.48, 100.04, 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 18 16.00 O 640 8.00 N 558 7.00 C 2093 6.00 H 3160 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 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 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 232.8 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: 772 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 8.7% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.790A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.989A pdb=" N GLN H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.115A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.762A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 377 through 380 Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.108A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP H 50 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN H 56 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.411A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.524A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) 70 hydrogen bonds defined for protein. 159 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: 1.24 Time building geometry restraints manager: 0.76 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: 3160 1.03 - 1.23: 4 1.23 - 1.42: 1500 1.42 - 1.62: 1866 1.62 - 1.82: 22 Bond restraints: 6552 Sorted by residual: bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.76e+00 bond pdb=" CA VAL A 524 " pdb=" CB VAL A 524 " ideal model delta sigma weight residual 1.530 1.542 -0.013 1.11e-02 8.12e+03 1.30e+00 bond pdb=" C PHE H 29 " pdb=" N THR H 30 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 1.07e+00 bond pdb=" CB PHE L 98 " pdb=" CG PHE L 98 " ideal model delta sigma weight residual 1.502 1.479 0.023 2.30e-02 1.89e+03 9.63e-01 bond pdb=" CA ILE H 48 " pdb=" CB ILE H 48 " ideal model delta sigma weight residual 1.545 1.532 0.013 1.45e-02 4.76e+03 8.24e-01 ... (remaining 6547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 11425 1.47 - 2.94: 273 2.94 - 4.40: 38 4.40 - 5.87: 5 5.87 - 7.34: 2 Bond angle restraints: 11743 Sorted by residual: angle pdb=" N ILE H 48 " pdb=" CA ILE H 48 " pdb=" C ILE H 48 " ideal model delta sigma weight residual 111.62 104.28 7.34 7.90e-01 1.60e+00 8.63e+01 angle pdb=" N TRP H 47 " pdb=" CA TRP H 47 " pdb=" C TRP H 47 " ideal model delta sigma weight residual 110.24 116.38 -6.14 1.30e+00 5.92e-01 2.23e+01 angle pdb=" N GLY A 381 " pdb=" CA GLY A 381 " pdb=" C GLY A 381 " ideal model delta sigma weight residual 113.58 109.75 3.83 1.07e+00 8.73e-01 1.28e+01 angle pdb=" C TRP H 47 " pdb=" CA TRP H 47 " pdb=" CB TRP H 47 " ideal model delta sigma weight residual 109.64 104.40 5.24 1.77e+00 3.19e-01 8.76e+00 angle pdb=" C PRO A 463 " pdb=" N PHE A 464 " pdb=" CA PHE A 464 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.79e+00 ... (remaining 11738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 2777 16.08 - 32.15: 262 32.15 - 48.22: 80 48.22 - 64.30: 37 64.30 - 80.37: 8 Dihedral angle restraints: 3164 sinusoidal: 1677 harmonic: 1487 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 28.65 64.35 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -143.11 57.11 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS H 97 " pdb=" SG CYS H 97 " pdb=" SG CYS H 100B" pdb=" CB CYS H 100B" ideal model delta sinusoidal sigma weight residual -86.00 -45.36 -40.64 1 1.00e+01 1.00e-02 2.32e+01 ... (remaining 3161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 349 0.042 - 0.083: 101 0.083 - 0.125: 36 0.125 - 0.167: 5 0.167 - 0.209: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE H 48 " pdb=" N ILE H 48 " pdb=" C ILE H 48 " pdb=" CB ILE H 48 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA TRP H 47 " pdb=" N TRP H 47 " pdb=" C TRP H 47 " pdb=" CB TRP H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" C PRO L 80 " pdb=" CB PRO L 80 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 489 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.022 2.00e-02 2.50e+03 1.06e-02 4.46e+00 pdb=" CG TRP H 47 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP H 47 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP H 47 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 47 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP H 47 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 94 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO L 95 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 35 " 0.009 2.00e-02 2.50e+03 7.85e-03 2.46e+00 pdb=" CG TRP L 35 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP L 35 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP L 35 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 35 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 35 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 35 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 35 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP L 35 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP L 35 " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP L 35 " 0.002 2.00e-02 2.50e+03 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 210 2.10 - 2.72: 11442 2.72 - 3.35: 18874 3.35 - 3.97: 24223 3.97 - 4.60: 37018 Nonbonded interactions: 91767 Sorted by model distance: nonbonded pdb=" H TYR A 453 " pdb=" O GLN A 493 " model vdw 1.473 2.450 nonbonded pdb="HH22 ARG H 66 " pdb=" OD2 ASP H 86 " model vdw 1.594 2.450 nonbonded pdb=" H GLN A 498 " pdb=" OD1 ASN A 501 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLN H 6 " pdb=" H GLY H 106 " model vdw 1.608 2.450 nonbonded pdb=" O SER L 76 " pdb=" HE ARG L 77 " model vdw 1.641 2.450 ... (remaining 91762 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 group one per residue 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: 13.220 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: 0.030 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.850 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 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 0.041 3399 Z= 0.150 Angle : 0.679 7.339 4622 Z= 0.403 Chirality : 0.045 0.209 492 Planarity : 0.005 0.046 599 Dihedral : 13.712 80.375 1206 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.68 (0.37), residues: 421 helix: -4.42 (0.50), residues: 19 sheet: -2.65 (0.38), residues: 124 loop : -2.28 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 18 TYR 0.027 0.002 TYR L 87 PHE 0.017 0.002 PHE A 347 TRP 0.033 0.003 TRP H 47 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3392) covalent geometry : angle 0.67674 ( 4608) SS BOND : bond 0.00354 ( 7) SS BOND : angle 1.18312 ( 14) hydrogen bonds : bond 0.27698 ( 70) hydrogen bonds : angle 11.56181 ( 159) *********************** 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 85 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7500 (tmm160) cc_final: 0.7146 (tmt170) REVERT: A 351 TYR cc_start: 0.7985 (p90) cc_final: 0.7743 (p90) REVERT: A 394 ASN cc_start: 0.8238 (m110) cc_final: 0.7884 (m110) REVERT: A 512 VAL cc_start: 0.8767 (t) cc_final: 0.8529 (t) REVERT: H 2 MET cc_start: 0.5820 (mmp) cc_final: 0.5591 (mmp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1772 time to fit residues: 17.5762 Evaluate side-chains 70 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.106624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100204 restraints weight = 22051.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.102682 restraints weight = 10386.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.104111 restraints weight = 5467.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.104938 restraints weight = 3128.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.105323 restraints weight = 1941.620| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 3399 Z= 0.235 Angle : 0.706 16.345 4622 Z= 0.375 Chirality : 0.045 0.245 492 Planarity : 0.005 0.041 599 Dihedral : 6.067 29.441 471 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.96 % Favored : 85.04 % Rotamer: Outliers : 0.28 % Allowed : 4.71 % Favored : 95.01 % 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: -3.78 (0.37), residues: 421 helix: -4.15 (0.55), residues: 19 sheet: -2.68 (0.39), residues: 118 loop : -2.43 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.013 0.002 TYR H 90 PHE 0.011 0.002 PHE A 347 TRP 0.018 0.002 TRP H 47 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 3392) covalent geometry : angle 0.68851 ( 4608) SS BOND : bond 0.00817 ( 7) SS BOND : angle 2.95009 ( 14) hydrogen bonds : bond 0.03858 ( 70) hydrogen bonds : angle 8.78486 ( 159) *********************** 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 85 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.118 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: symmetry clash REVERT: A 473 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8342 (t80) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1691 time to fit residues: 16.9012 Evaluate side-chains 74 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 39 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 0 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.105625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099245 restraints weight = 21985.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101768 restraints weight = 10190.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.103149 restraints weight = 5302.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.104013 restraints weight = 3059.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.104488 restraints weight = 1841.237| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 3399 Z= 0.231 Angle : 0.695 14.450 4622 Z= 0.372 Chirality : 0.045 0.219 492 Planarity : 0.005 0.046 599 Dihedral : 6.059 29.496 471 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.25 % Favored : 85.75 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -4.03 (0.37), residues: 421 helix: -3.64 (0.67), residues: 27 sheet: -2.91 (0.39), residues: 119 loop : -2.57 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 38 TYR 0.013 0.002 TYR L 87 PHE 0.013 0.002 PHE A 392 TRP 0.017 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 3392) covalent geometry : angle 0.67556 ( 4608) SS BOND : bond 0.00662 ( 7) SS BOND : angle 3.02764 ( 14) hydrogen bonds : bond 0.04028 ( 70) hydrogen bonds : angle 8.31657 ( 159) *********************** 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 89 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.131 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7312 (tmm160) cc_final: 0.6472 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1980 time to fit residues: 20.4006 Evaluate side-chains 76 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.0170 chunk 11 optimal weight: 0.3980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 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 = 0.3680 r_free = 0.3680 target = 0.106533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100652 restraints weight = 22125.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.102958 restraints weight = 10554.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.104284 restraints weight = 5585.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.105070 restraints weight = 3218.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.105520 restraints weight = 1951.374| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 3399 Z= 0.189 Angle : 0.652 12.983 4622 Z= 0.347 Chirality : 0.044 0.197 492 Planarity : 0.004 0.044 599 Dihedral : 5.952 28.851 471 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.73 % Favored : 85.27 % Rotamer: Outliers : 0.28 % Allowed : 1.39 % Favored : 98.34 % 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: -3.72 (0.38), residues: 421 helix: -3.97 (0.64), residues: 19 sheet: -2.95 (0.41), residues: 110 loop : -2.28 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 71 TYR 0.012 0.002 TYR A 489 PHE 0.009 0.001 PHE A 400 TRP 0.016 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 3392) covalent geometry : angle 0.63763 ( 4608) SS BOND : bond 0.00505 ( 7) SS BOND : angle 2.57234 ( 14) hydrogen bonds : bond 0.03740 ( 70) hydrogen bonds : angle 8.08606 ( 159) *********************** 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 95 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.108 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7159 (tmm160) cc_final: 0.6646 (ptm-80) outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.1859 time to fit residues: 20.5152 Evaluate side-chains 81 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN L 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.094762 restraints weight = 22629.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.097122 restraints weight = 11185.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.098455 restraints weight = 6047.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.099234 restraints weight = 3579.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.099745 restraints weight = 2279.595| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 3399 Z= 0.305 Angle : 0.736 12.041 4622 Z= 0.400 Chirality : 0.045 0.194 492 Planarity : 0.005 0.047 599 Dihedral : 6.452 31.671 471 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.76 % Favored : 81.24 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.98 (0.38), residues: 421 helix: -4.01 (0.60), residues: 19 sheet: -3.09 (0.42), residues: 112 loop : -2.48 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 44 TYR 0.013 0.002 TYR A 351 PHE 0.016 0.002 PHE A 400 TRP 0.015 0.002 TRP H 47 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00676 ( 3392) covalent geometry : angle 0.72170 ( 4608) SS BOND : bond 0.00464 ( 7) SS BOND : angle 2.74947 ( 14) hydrogen bonds : bond 0.03797 ( 70) hydrogen bonds : angle 8.23650 ( 159) *********************** 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 92 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.186 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7176 (tmm160) cc_final: 0.6646 (ptm-80) REVERT: H 105 GLN cc_start: 0.8292 (pt0) cc_final: 0.8027 (pt0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1797 time to fit residues: 19.4849 Evaluate side-chains 79 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0980 chunk 22 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 15 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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 = 0.3638 r_free = 0.3638 target = 0.104203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097588 restraints weight = 22136.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.100112 restraints weight = 10866.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.101574 restraints weight = 5868.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.102427 restraints weight = 3424.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.102846 restraints weight = 2131.578| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 3399 Z= 0.202 Angle : 0.674 12.057 4622 Z= 0.362 Chirality : 0.045 0.172 492 Planarity : 0.005 0.047 599 Dihedral : 6.238 29.725 471 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.54 % Favored : 86.46 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: -3.94 (0.38), residues: 421 helix: -3.90 (0.67), residues: 19 sheet: -3.22 (0.42), residues: 110 loop : -2.40 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.021 0.002 TYR A 489 PHE 0.013 0.002 PHE A 400 TRP 0.039 0.003 TRP L 35 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 3392) covalent geometry : angle 0.66187 ( 4608) SS BOND : bond 0.00560 ( 7) SS BOND : angle 2.38457 ( 14) hydrogen bonds : bond 0.03713 ( 70) hydrogen bonds : angle 7.87822 ( 159) *********************** 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 91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.139 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7144 (tmm160) cc_final: 0.6608 (ptm-80) REVERT: H 105 GLN cc_start: 0.8255 (pt0) cc_final: 0.7957 (pt0) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1784 time to fit residues: 19.0730 Evaluate side-chains 77 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 6 optimal weight: 0.0980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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 = 0.3656 r_free = 0.3656 target = 0.105230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098882 restraints weight = 21553.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101271 restraints weight = 10648.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.102649 restraints weight = 5805.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.103484 restraints weight = 3465.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.104005 restraints weight = 2186.726| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 3399 Z= 0.196 Angle : 0.675 11.010 4622 Z= 0.364 Chirality : 0.045 0.163 492 Planarity : 0.005 0.045 599 Dihedral : 6.237 30.667 471 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.96 % Favored : 85.04 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -3.90 (0.38), residues: 421 helix: -3.85 (0.72), residues: 19 sheet: -3.20 (0.43), residues: 110 loop : -2.36 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.019 0.002 TYR A 380 PHE 0.012 0.002 PHE A 392 TRP 0.031 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 3392) covalent geometry : angle 0.66358 ( 4608) SS BOND : bond 0.00615 ( 7) SS BOND : angle 2.34604 ( 14) hydrogen bonds : bond 0.03595 ( 70) hydrogen bonds : angle 7.80778 ( 159) *********************** 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 92 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.161 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7143 (tmm160) cc_final: 0.6611 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1628 time to fit residues: 17.6613 Evaluate side-chains 77 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 24 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098658 restraints weight = 21727.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101306 restraints weight = 10539.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.102804 restraints weight = 5670.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.103703 restraints weight = 3321.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.104144 restraints weight = 2092.505| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 3399 Z= 0.187 Angle : 0.659 10.438 4622 Z= 0.353 Chirality : 0.045 0.161 492 Planarity : 0.005 0.045 599 Dihedral : 6.159 29.638 471 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.01 % Favored : 85.99 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -3.79 (0.39), residues: 421 helix: -3.73 (0.81), residues: 19 sheet: -3.21 (0.43), residues: 114 loop : -2.22 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.018 0.002 TYR A 453 PHE 0.012 0.002 PHE L 71 TRP 0.027 0.002 TRP H 47 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 3392) covalent geometry : angle 0.64654 ( 4608) SS BOND : bond 0.00618 ( 7) SS BOND : angle 2.37468 ( 14) hydrogen bonds : bond 0.03541 ( 70) hydrogen bonds : angle 7.69287 ( 159) *********************** 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 91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.170 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7150 (tmm160) cc_final: 0.6686 (ptm160) REVERT: A 427 ASP cc_start: 0.7218 (m-30) cc_final: 0.6996 (m-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1802 time to fit residues: 19.3327 Evaluate side-chains 78 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 0.0670 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 9 optimal weight: 0.0770 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 overall best weight: 0.1874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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 = 0.3691 r_free = 0.3691 target = 0.107114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100487 restraints weight = 21940.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.103010 restraints weight = 10730.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.104478 restraints weight = 5793.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.105345 restraints weight = 3392.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.105777 restraints weight = 2128.790| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3399 Z= 0.151 Angle : 0.650 11.113 4622 Z= 0.348 Chirality : 0.045 0.143 492 Planarity : 0.005 0.045 599 Dihedral : 6.091 30.113 471 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.30 % Favored : 86.70 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.69 (0.39), residues: 421 helix: -3.64 (0.88), residues: 19 sheet: -3.18 (0.45), residues: 114 loop : -2.14 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.023 0.002 TYR A 473 PHE 0.012 0.002 PHE L 71 TRP 0.029 0.002 TRP H 47 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3392) covalent geometry : angle 0.63940 ( 4608) SS BOND : bond 0.00453 ( 7) SS BOND : angle 2.20122 ( 14) hydrogen bonds : bond 0.03535 ( 70) hydrogen bonds : angle 7.42652 ( 159) *********************** 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 91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.104 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7122 (tmm160) cc_final: 0.6627 (ptm-80) REVERT: A 427 ASP cc_start: 0.7167 (m-30) cc_final: 0.6945 (m-30) REVERT: A 452 LEU cc_start: 0.8411 (mt) cc_final: 0.8089 (mt) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1893 time to fit residues: 20.1422 Evaluate side-chains 75 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 9 optimal weight: 0.0980 chunk 33 optimal weight: 0.2980 chunk 18 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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 = 0.3685 r_free = 0.3685 target = 0.106892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.100034 restraints weight = 21456.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.102672 restraints weight = 10286.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.104167 restraints weight = 5489.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.104956 restraints weight = 3182.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.105497 restraints weight = 2149.565| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3399 Z= 0.170 Angle : 0.658 11.219 4622 Z= 0.352 Chirality : 0.045 0.147 492 Planarity : 0.005 0.046 599 Dihedral : 6.036 31.561 471 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.73 % Favored : 85.27 % 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 : 0.25 % 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: -3.66 (0.40), residues: 421 helix: -3.44 (0.98), residues: 19 sheet: -3.19 (0.45), residues: 114 loop : -2.11 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 18 TYR 0.021 0.002 TYR A 473 PHE 0.011 0.002 PHE L 71 TRP 0.029 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 3392) covalent geometry : angle 0.64775 ( 4608) SS BOND : bond 0.00561 ( 7) SS BOND : angle 2.21885 ( 14) hydrogen bonds : bond 0.03491 ( 70) hydrogen bonds : angle 7.38587 ( 159) ********************** 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 91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.170 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7119 (tmm160) cc_final: 0.6625 (ptm160) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1748 time to fit residues: 18.8360 Evaluate side-chains 78 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 13 optimal weight: 0.2980 chunk 8 optimal weight: 0.3980 chunk 23 optimal weight: 0.0980 chunk 16 optimal weight: 0.0770 chunk 30 optimal weight: 0.4980 chunk 28 optimal weight: 0.0070 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 24 optimal weight: 0.2980 overall best weight: 0.1356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.108584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100622 restraints weight = 21566.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.103762 restraints weight = 10136.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.105559 restraints weight = 5263.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.106596 restraints weight = 2969.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.107216 restraints weight = 1811.631| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3399 Z= 0.139 Angle : 0.651 10.784 4622 Z= 0.349 Chirality : 0.045 0.148 492 Planarity : 0.005 0.046 599 Dihedral : 5.888 32.608 471 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.57 (0.40), residues: 421 helix: -3.35 (1.02), residues: 19 sheet: -3.16 (0.45), residues: 114 loop : -2.04 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.014 0.002 TYR L 87 PHE 0.011 0.002 PHE L 71 TRP 0.032 0.002 TRP H 47 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3392) covalent geometry : angle 0.64085 ( 4608) SS BOND : bond 0.00532 ( 7) SS BOND : angle 2.20393 ( 14) hydrogen bonds : bond 0.03518 ( 70) hydrogen bonds : angle 7.27414 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2227.44 seconds wall clock time: 38 minutes 30.06 seconds (2310.06 seconds total)