Starting phenix.real_space_refine on Wed Sep 17 05:18:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xef_38288/09_2025/8xef_38288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xef_38288/09_2025/8xef_38288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xef_38288/09_2025/8xef_38288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xef_38288/09_2025/8xef_38288.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xef_38288/09_2025/8xef_38288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xef_38288/09_2025/8xef_38288.map" } resolution = 4.41 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= 0.002 sd= 0.021 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 19 5.16 5 C 3173 2.51 5 N 840 2.21 5 O 975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5007 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1548 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 96} Chain: "D" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 917 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 1.62, per 1000 atoms: 0.32 Number of scatterers: 5007 At special positions: 0 Unit cell: (63.99, 109.35, 123.93, 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 19 16.00 O 975 8.00 N 840 7.00 C 3173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " 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 C 22 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 221.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 15 sheets defined 5.9% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.799A pdb=" N ILE A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.583A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.730A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.522A pdb=" N GLN D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.627A pdb=" N ALA D 92 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 403 Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.736A pdb=" N SER B 60 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR B 52 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TRP B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG B 40 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 51 " --> pdb=" O TRP B 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 69 through 74 Processing sheet with id=AA7, first strand: chain 'C' and resid 18 through 23 removed outlier: 3.832A pdb=" N THR C 73 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.469A pdb=" N LEU C 45 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN C 36 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 47 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS C 33 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR C 35 " --> pdb=" O TYR C 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.469A pdb=" N LEU C 45 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN C 36 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 47 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS C 33 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR C 35 " --> pdb=" O TYR C 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.755A pdb=" N VAL D 18 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 51 removed outlier: 3.625A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.689A pdb=" N ARG E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.007A pdb=" N THR E 96 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 48 through 49 removed outlier: 3.593A pdb=" N ASN E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) 108 hydrogen bonds defined for protein. 243 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: 0.73 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1580 1.34 - 1.46: 1204 1.46 - 1.58: 2334 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 5140 Sorted by residual: bond pdb=" CG1 ILE B 39 " pdb=" CD1 ILE B 39 " ideal model delta sigma weight residual 1.513 1.424 0.089 3.90e-02 6.57e+02 5.23e+00 bond pdb=" CB ILE B 39 " pdb=" CG2 ILE B 39 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.13e+00 bond pdb=" CA THR D 58 " pdb=" CB THR D 58 " ideal model delta sigma weight residual 1.535 1.559 -0.023 1.64e-02 3.72e+03 2.01e+00 bond pdb=" CB GLN D 1 " pdb=" CG GLN D 1 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 1.326 1.343 -0.017 1.44e-02 4.82e+03 1.40e+00 ... (remaining 5135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 6638 1.98 - 3.96: 279 3.96 - 5.94: 68 5.94 - 7.92: 15 7.92 - 9.89: 4 Bond angle restraints: 7004 Sorted by residual: angle pdb=" CA CYS E 23 " pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " ideal model delta sigma weight residual 114.40 124.29 -9.89 2.30e+00 1.89e-01 1.85e+01 angle pdb=" C THR E 30 " pdb=" N ASN E 31 " pdb=" CA ASN E 31 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY A 476 " pdb=" N ASN A 477 " pdb=" CA ASN A 477 " ideal model delta sigma weight residual 121.54 129.18 -7.64 1.91e+00 2.74e-01 1.60e+01 angle pdb=" C ARG E 22 " pdb=" N CYS E 23 " pdb=" CA CYS E 23 " ideal model delta sigma weight residual 122.94 117.56 5.38 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C THR B 32 " pdb=" N THR B 33 " pdb=" CA THR B 33 " ideal model delta sigma weight residual 121.54 128.35 -6.81 1.91e+00 2.74e-01 1.27e+01 ... (remaining 6999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2762 17.94 - 35.89: 209 35.89 - 53.83: 31 53.83 - 71.78: 9 71.78 - 89.72: 2 Dihedral angle restraints: 3013 sinusoidal: 1147 harmonic: 1866 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 27.60 65.40 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CA CYS E 23 " pdb=" C CYS E 23 " pdb=" N GLN E 24 " pdb=" CA GLN E 24 " ideal model delta harmonic sigma weight residual -180.00 -145.97 -34.03 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 87 " pdb=" CB CYS C 87 " ideal model delta sinusoidal sigma weight residual 93.00 151.09 -58.09 1 1.00e+01 1.00e-02 4.52e+01 ... (remaining 3010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 650 0.084 - 0.168: 95 0.168 - 0.251: 11 0.251 - 0.335: 0 0.335 - 0.419: 2 Chirality restraints: 758 Sorted by residual: chirality pdb=" CB ILE E 83 " pdb=" CA ILE E 83 " pdb=" CG1 ILE E 83 " pdb=" CG2 ILE E 83 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CB ILE D 52 " pdb=" CA ILE D 52 " pdb=" CG1 ILE D 52 " pdb=" CG2 ILE D 52 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CG LEU D 108 " pdb=" CB LEU D 108 " pdb=" CD1 LEU D 108 " pdb=" CD2 LEU D 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 755 not shown) Planarity restraints: 907 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 13 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO B 14 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 37 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" CD GLN C 37 " 0.047 2.00e-02 2.50e+03 pdb=" OE1 GLN C 37 " -0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN C 37 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 58 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C THR D 58 " 0.034 2.00e-02 2.50e+03 pdb=" O THR D 58 " -0.013 2.00e-02 2.50e+03 pdb=" N HIS D 59 " -0.012 2.00e-02 2.50e+03 ... (remaining 904 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 46 2.49 - 3.09: 3507 3.09 - 3.69: 8282 3.69 - 4.30: 10984 4.30 - 4.90: 17432 Nonbonded interactions: 40251 Sorted by model distance: nonbonded pdb=" CD1 PHE A 456 " pdb=" CE LYS D 31 " model vdw 1.886 2.992 nonbonded pdb=" OH TYR A 421 " pdb=" CD LYS D 31 " model vdw 2.251 3.440 nonbonded pdb=" O LEU D 108 " pdb=" OH TYR E 36 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR C 17 " pdb=" NH2 ARG C 19 " model vdw 2.270 3.120 nonbonded pdb=" OH TYR B 52 " pdb=" O ASP C 95 " model vdw 2.294 3.040 ... (remaining 40246 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: 1.420 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.050 Find NCS groups from input model: 0.040 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 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 : 0.006 0.313 5147 Z= 0.482 Angle : 1.000 9.895 7016 Z= 0.527 Chirality : 0.062 0.419 758 Planarity : 0.008 0.080 907 Dihedral : 12.948 89.720 1811 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.86 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: -3.14 (0.31), residues: 639 helix: -3.98 (0.52), residues: 33 sheet: -1.49 (0.35), residues: 204 loop : -2.33 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 76 TYR 0.025 0.002 TYR B 35 PHE 0.022 0.003 PHE A 338 TRP 0.033 0.003 TRP B 36 HIS 0.011 0.002 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 5140) covalent geometry : angle 0.99656 ( 7004) SS BOND : bond 0.00674 ( 6) SS BOND : angle 2.35868 ( 12) hydrogen bonds : bond 0.20006 ( 98) hydrogen bonds : angle 10.29185 ( 243) Misc. bond : bond 0.31308 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.241 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 338 PHE cc_start: 0.8496 (t80) cc_final: 0.7807 (t80) REVERT: A 339 HIS cc_start: 0.8418 (m170) cc_final: 0.7240 (m170) REVERT: A 354 ASN cc_start: 0.8668 (m-40) cc_final: 0.8267 (m-40) REVERT: A 368 ILE cc_start: 0.9307 (mp) cc_final: 0.9061 (mp) REVERT: A 396 TYR cc_start: 0.8505 (m-10) cc_final: 0.8302 (m-80) REVERT: B 103 TYR cc_start: 0.8318 (p90) cc_final: 0.8048 (p90) REVERT: B 108 PHE cc_start: 0.8482 (m-80) cc_final: 0.7587 (m-80) REVERT: C 16 LYS cc_start: 0.9618 (tmtt) cc_final: 0.9403 (tmtt) REVERT: C 35 TYR cc_start: 0.8536 (m-80) cc_final: 0.7687 (m-80) REVERT: C 49 TYR cc_start: 0.9200 (m-80) cc_final: 0.8943 (m-80) REVERT: C 61 PHE cc_start: 0.9103 (m-10) cc_final: 0.8835 (m-80) REVERT: D 71 THR cc_start: 0.9290 (p) cc_final: 0.9082 (p) REVERT: D 81 MET cc_start: 0.9051 (mmp) cc_final: 0.8541 (mmp) REVERT: D 83 LEU cc_start: 0.9299 (tp) cc_final: 0.9046 (tp) REVERT: D 100 GLU cc_start: 0.7745 (mp0) cc_final: 0.7001 (mp0) REVERT: E 47 LEU cc_start: 0.9515 (mm) cc_final: 0.9187 (mm) REVERT: E 71 PHE cc_start: 0.8686 (m-80) cc_final: 0.8166 (m-80) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1016 time to fit residues: 17.5533 Evaluate side-chains 101 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 79 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 = 0.2783 r_free = 0.2783 target = 0.034986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.025093 restraints weight = 41886.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.026482 restraints weight = 23464.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.027501 restraints weight = 15789.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.028241 restraints weight = 11757.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.028804 restraints weight = 9394.527| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 5147 Z= 0.293 Angle : 0.800 10.469 7016 Z= 0.422 Chirality : 0.047 0.214 758 Planarity : 0.007 0.059 907 Dihedral : 6.470 32.828 710 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 28.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.64 % Favored : 89.20 % Rotamer: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: -3.30 (0.30), residues: 639 helix: -4.12 (0.45), residues: 32 sheet: -1.75 (0.33), residues: 206 loop : -2.35 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 355 TYR 0.019 0.003 TYR D 32 PHE 0.032 0.003 PHE E 87 TRP 0.016 0.003 TRP C 90 HIS 0.006 0.002 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00614 ( 5140) covalent geometry : angle 0.79445 ( 7004) SS BOND : bond 0.00663 ( 6) SS BOND : angle 2.44917 ( 12) hydrogen bonds : bond 0.04693 ( 98) hydrogen bonds : angle 7.65553 ( 243) Misc. bond : bond 0.00227 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8452 (t80) cc_final: 0.8104 (t80) REVERT: A 356 LYS cc_start: 0.9624 (tptp) cc_final: 0.9303 (tptp) REVERT: A 396 TYR cc_start: 0.8720 (m-10) cc_final: 0.8433 (m-80) REVERT: B 56 ASN cc_start: 0.9208 (m-40) cc_final: 0.8924 (m-40) REVERT: B 57 TRP cc_start: 0.9574 (m-90) cc_final: 0.9302 (m-90) REVERT: B 100 PHE cc_start: 0.7873 (m-80) cc_final: 0.7236 (m-80) REVERT: B 108 PHE cc_start: 0.8854 (m-80) cc_final: 0.7729 (m-80) REVERT: B 110 PHE cc_start: 0.9199 (m-80) cc_final: 0.8729 (m-80) REVERT: B 111 ASP cc_start: 0.9310 (t0) cc_final: 0.8971 (t0) REVERT: C 35 TYR cc_start: 0.8665 (m-80) cc_final: 0.7713 (m-80) REVERT: C 49 TYR cc_start: 0.9400 (m-80) cc_final: 0.8777 (m-80) REVERT: C 85 TYR cc_start: 0.9217 (m-80) cc_final: 0.8761 (m-80) REVERT: D 51 ASN cc_start: 0.9566 (t0) cc_final: 0.9344 (t0) REVERT: D 80 TYR cc_start: 0.9319 (m-80) cc_final: 0.9068 (m-80) REVERT: D 81 MET cc_start: 0.9305 (mmp) cc_final: 0.8869 (mmp) REVERT: E 70 ASP cc_start: 0.9525 (m-30) cc_final: 0.9285 (t0) REVERT: E 87 PHE cc_start: 0.9318 (m-80) cc_final: 0.8679 (m-80) REVERT: E 93 ASP cc_start: 0.9208 (m-30) cc_final: 0.8722 (p0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0846 time to fit residues: 12.7507 Evaluate side-chains 83 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 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 = 0.2800 r_free = 0.2800 target = 0.035641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.025773 restraints weight = 42236.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.027218 restraints weight = 22636.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.028270 restraints weight = 14934.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.029038 restraints weight = 10995.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.029609 restraints weight = 8706.218| |-----------------------------------------------------------------------------| r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5147 Z= 0.194 Angle : 0.684 6.786 7016 Z= 0.361 Chirality : 0.047 0.233 758 Planarity : 0.006 0.052 907 Dihedral : 6.072 24.259 710 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.86 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -3.33 (0.31), residues: 639 helix: -3.90 (0.53), residues: 32 sheet: -1.78 (0.33), residues: 208 loop : -2.39 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 18 TYR 0.012 0.002 TYR A 473 PHE 0.018 0.002 PHE B 100 TRP 0.028 0.002 TRP D 47 HIS 0.004 0.001 HIS C 33 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 5140) covalent geometry : angle 0.68102 ( 7004) SS BOND : bond 0.00460 ( 6) SS BOND : angle 1.73044 ( 12) hydrogen bonds : bond 0.04070 ( 98) hydrogen bonds : angle 7.11212 ( 243) Misc. bond : bond 0.00313 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8443 (t80) cc_final: 0.8093 (t80) REVERT: A 396 TYR cc_start: 0.8746 (m-10) cc_final: 0.8485 (m-80) REVERT: B 56 ASN cc_start: 0.9230 (m-40) cc_final: 0.8954 (m-40) REVERT: B 57 TRP cc_start: 0.9564 (m-90) cc_final: 0.9313 (m-90) REVERT: B 100 PHE cc_start: 0.7666 (m-80) cc_final: 0.7314 (m-80) REVERT: B 108 PHE cc_start: 0.8825 (m-80) cc_final: 0.7693 (m-80) REVERT: B 110 PHE cc_start: 0.9266 (m-80) cc_final: 0.8783 (m-80) REVERT: B 111 ASP cc_start: 0.9256 (t0) cc_final: 0.8957 (t0) REVERT: C 35 TYR cc_start: 0.8666 (m-80) cc_final: 0.7930 (m-80) REVERT: C 49 TYR cc_start: 0.9400 (m-80) cc_final: 0.9026 (m-80) REVERT: C 85 TYR cc_start: 0.9157 (m-80) cc_final: 0.8820 (m-80) REVERT: D 51 ASN cc_start: 0.9623 (t0) cc_final: 0.9335 (t0) REVERT: D 80 TYR cc_start: 0.9305 (m-80) cc_final: 0.9032 (m-80) REVERT: D 81 MET cc_start: 0.9173 (mmp) cc_final: 0.8751 (mmm) REVERT: E 47 LEU cc_start: 0.9451 (mm) cc_final: 0.9233 (mm) REVERT: E 70 ASP cc_start: 0.9510 (m-30) cc_final: 0.9294 (t0) REVERT: E 87 PHE cc_start: 0.9420 (m-80) cc_final: 0.8756 (m-10) REVERT: E 93 ASP cc_start: 0.9320 (m-30) cc_final: 0.8872 (p0) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0765 time to fit residues: 11.2437 Evaluate side-chains 82 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** 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 = 0.2806 r_free = 0.2806 target = 0.035702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.025820 restraints weight = 40446.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.027300 restraints weight = 21913.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.028366 restraints weight = 14495.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.029148 restraints weight = 10680.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.029726 restraints weight = 8465.254| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5147 Z= 0.158 Angle : 0.697 8.004 7016 Z= 0.364 Chirality : 0.047 0.230 758 Planarity : 0.005 0.048 907 Dihedral : 5.813 30.054 710 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.11 % Favored : 88.73 % Rotamer: Outliers : 0.18 % Allowed : 4.93 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: -3.25 (0.31), residues: 639 helix: -3.47 (0.66), residues: 32 sheet: -1.77 (0.34), residues: 205 loop : -2.34 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 98 TYR 0.046 0.002 TYR A 421 PHE 0.029 0.002 PHE A 456 TRP 0.026 0.002 TRP D 47 HIS 0.003 0.001 HIS C 33 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5140) covalent geometry : angle 0.69246 ( 7004) SS BOND : bond 0.00545 ( 6) SS BOND : angle 1.97063 ( 12) hydrogen bonds : bond 0.03526 ( 98) hydrogen bonds : angle 6.85652 ( 243) Misc. bond : bond 0.00727 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8480 (t80) cc_final: 0.8132 (t80) REVERT: A 396 TYR cc_start: 0.8730 (m-10) cc_final: 0.8426 (m-80) REVERT: B 56 ASN cc_start: 0.9215 (m-40) cc_final: 0.8943 (m-40) REVERT: B 57 TRP cc_start: 0.9566 (m-90) cc_final: 0.9331 (m-90) REVERT: B 100 PHE cc_start: 0.7771 (m-80) cc_final: 0.7388 (m-80) REVERT: B 108 PHE cc_start: 0.8860 (m-80) cc_final: 0.7608 (m-80) REVERT: B 110 PHE cc_start: 0.9261 (m-80) cc_final: 0.8734 (m-80) REVERT: C 35 TYR cc_start: 0.8669 (m-80) cc_final: 0.7988 (m-80) REVERT: C 49 TYR cc_start: 0.9362 (m-80) cc_final: 0.8970 (m-80) REVERT: D 51 ASN cc_start: 0.9624 (t0) cc_final: 0.9303 (t0) REVERT: D 80 TYR cc_start: 0.9295 (m-80) cc_final: 0.9030 (m-80) REVERT: D 81 MET cc_start: 0.9109 (mmp) cc_final: 0.8652 (mmm) REVERT: E 71 PHE cc_start: 0.8431 (m-80) cc_final: 0.7987 (m-80) REVERT: E 87 PHE cc_start: 0.9186 (m-80) cc_final: 0.8736 (m-10) REVERT: E 93 ASP cc_start: 0.9370 (m-30) cc_final: 0.8943 (m-30) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.0768 time to fit residues: 11.3413 Evaluate side-chains 88 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 38 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.2823 r_free = 0.2823 target = 0.036293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.026336 restraints weight = 41843.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.027805 restraints weight = 22716.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.028879 restraints weight = 15094.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.029667 restraints weight = 11156.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.030243 restraints weight = 8826.018| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5147 Z= 0.162 Angle : 0.714 11.730 7016 Z= 0.371 Chirality : 0.047 0.198 758 Planarity : 0.005 0.053 907 Dihedral : 5.763 24.758 710 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.95 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -3.25 (0.31), residues: 639 helix: -3.24 (0.73), residues: 32 sheet: -1.79 (0.33), residues: 210 loop : -2.35 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 98 TYR 0.035 0.002 TYR A 421 PHE 0.022 0.002 PHE A 456 TRP 0.042 0.002 TRP D 47 HIS 0.003 0.001 HIS C 33 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 5140) covalent geometry : angle 0.71163 ( 7004) SS BOND : bond 0.00487 ( 6) SS BOND : angle 1.61287 ( 12) hydrogen bonds : bond 0.03783 ( 98) hydrogen bonds : angle 6.55602 ( 243) Misc. bond : bond 0.00372 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.153 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 338 PHE cc_start: 0.8475 (t80) cc_final: 0.8116 (t80) REVERT: A 396 TYR cc_start: 0.8748 (m-10) cc_final: 0.8449 (m-80) REVERT: B 52 TYR cc_start: 0.9720 (p90) cc_final: 0.9418 (p90) REVERT: B 110 PHE cc_start: 0.9280 (m-80) cc_final: 0.8745 (m-80) REVERT: C 35 TYR cc_start: 0.8779 (m-80) cc_final: 0.7994 (m-80) REVERT: C 49 TYR cc_start: 0.9367 (m-80) cc_final: 0.8958 (m-80) REVERT: D 32 TYR cc_start: 0.8133 (m-10) cc_final: 0.7629 (m-80) REVERT: D 80 TYR cc_start: 0.9272 (m-80) cc_final: 0.9026 (m-80) REVERT: D 81 MET cc_start: 0.9095 (mmp) cc_final: 0.8681 (mmm) REVERT: E 42 LYS cc_start: 0.9738 (tppt) cc_final: 0.9535 (mmmt) REVERT: E 70 ASP cc_start: 0.9493 (m-30) cc_final: 0.9276 (t0) REVERT: E 87 PHE cc_start: 0.9358 (m-80) cc_final: 0.9145 (m-80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0799 time to fit residues: 11.7295 Evaluate side-chains 87 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.0270 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** 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 = 0.2855 r_free = 0.2855 target = 0.037154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.026949 restraints weight = 41133.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.028526 restraints weight = 22302.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.029653 restraints weight = 14720.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.030485 restraints weight = 10827.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.031099 restraints weight = 8527.079| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5147 Z= 0.132 Angle : 0.701 10.368 7016 Z= 0.362 Chirality : 0.049 0.327 758 Planarity : 0.005 0.048 907 Dihedral : 5.707 29.687 710 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.80 % Favored : 89.05 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -3.06 (0.32), residues: 639 helix: -3.11 (0.78), residues: 33 sheet: -1.67 (0.34), residues: 199 loop : -2.21 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 98 TYR 0.012 0.001 TYR A 421 PHE 0.022 0.001 PHE A 456 TRP 0.027 0.001 TRP D 47 HIS 0.003 0.001 HIS C 33 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5140) covalent geometry : angle 0.69663 ( 7004) SS BOND : bond 0.00664 ( 6) SS BOND : angle 1.93102 ( 12) hydrogen bonds : bond 0.03275 ( 98) hydrogen bonds : angle 6.21334 ( 243) Misc. bond : bond 0.00480 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8437 (t80) cc_final: 0.8079 (t80) REVERT: A 396 TYR cc_start: 0.8734 (m-10) cc_final: 0.8436 (m-80) REVERT: B 72 SER cc_start: 0.9507 (t) cc_final: 0.9300 (p) REVERT: B 103 TYR cc_start: 0.8680 (p90) cc_final: 0.8181 (p90) REVERT: B 108 PHE cc_start: 0.8881 (m-80) cc_final: 0.7763 (m-80) REVERT: B 110 PHE cc_start: 0.9268 (m-80) cc_final: 0.8489 (m-80) REVERT: B 111 ASP cc_start: 0.9192 (t0) cc_final: 0.8331 (m-30) REVERT: C 35 TYR cc_start: 0.8793 (m-80) cc_final: 0.7646 (m-80) REVERT: C 49 TYR cc_start: 0.9337 (m-80) cc_final: 0.8922 (m-80) REVERT: D 81 MET cc_start: 0.9161 (mmp) cc_final: 0.8707 (mmm) REVERT: E 4 MET cc_start: 0.7999 (tpp) cc_final: 0.7624 (tpp) REVERT: E 34 ASN cc_start: 0.8718 (m-40) cc_final: 0.7999 (m110) REVERT: E 70 ASP cc_start: 0.9422 (m-30) cc_final: 0.9179 (t0) REVERT: E 71 PHE cc_start: 0.8540 (m-80) cc_final: 0.8181 (m-10) REVERT: E 93 ASP cc_start: 0.8853 (p0) cc_final: 0.8366 (p0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0779 time to fit residues: 11.9852 Evaluate side-chains 89 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 chunk 36 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.2829 r_free = 0.2829 target = 0.035944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.025737 restraints weight = 41216.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.027208 restraints weight = 22951.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.028293 restraints weight = 15420.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.029068 restraints weight = 11483.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.029666 restraints weight = 9169.620| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5147 Z= 0.149 Angle : 0.705 15.784 7016 Z= 0.360 Chirality : 0.048 0.271 758 Planarity : 0.005 0.060 907 Dihedral : 5.456 23.593 710 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.64 % Favored : 89.20 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -3.04 (0.32), residues: 639 helix: -3.05 (0.78), residues: 33 sheet: -1.64 (0.33), residues: 198 loop : -2.21 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 98 TYR 0.030 0.002 TYR A 421 PHE 0.018 0.002 PHE A 456 TRP 0.031 0.002 TRP D 47 HIS 0.003 0.001 HIS C 33 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5140) covalent geometry : angle 0.70325 ( 7004) SS BOND : bond 0.00387 ( 6) SS BOND : angle 1.50096 ( 12) hydrogen bonds : bond 0.03530 ( 98) hydrogen bonds : angle 6.01035 ( 243) Misc. bond : bond 0.00664 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8450 (t80) cc_final: 0.8091 (t80) REVERT: A 396 TYR cc_start: 0.8764 (m-10) cc_final: 0.8413 (m-80) REVERT: A 465 GLU cc_start: 0.8288 (pt0) cc_final: 0.7929 (pt0) REVERT: B 52 TYR cc_start: 0.9774 (p90) cc_final: 0.9299 (p90) REVERT: B 72 SER cc_start: 0.9559 (t) cc_final: 0.9335 (p) REVERT: B 108 PHE cc_start: 0.8960 (m-80) cc_final: 0.7801 (m-80) REVERT: B 110 PHE cc_start: 0.9383 (m-80) cc_final: 0.8564 (m-80) REVERT: B 111 ASP cc_start: 0.9246 (t0) cc_final: 0.8432 (m-30) REVERT: C 35 TYR cc_start: 0.8843 (m-80) cc_final: 0.7692 (m-80) REVERT: C 49 TYR cc_start: 0.9428 (m-80) cc_final: 0.8983 (m-80) REVERT: D 34 ILE cc_start: 0.9690 (mm) cc_final: 0.9457 (tp) REVERT: D 51 ASN cc_start: 0.9611 (t0) cc_final: 0.9359 (t0) REVERT: D 71 THR cc_start: 0.9216 (p) cc_final: 0.8956 (p) REVERT: D 81 MET cc_start: 0.9261 (mmp) cc_final: 0.8723 (mmm) REVERT: E 50 ASP cc_start: 0.9692 (m-30) cc_final: 0.9357 (t0) REVERT: E 70 ASP cc_start: 0.9406 (m-30) cc_final: 0.9151 (t0) REVERT: E 87 PHE cc_start: 0.9282 (m-80) cc_final: 0.9066 (m-80) REVERT: E 93 ASP cc_start: 0.9051 (p0) cc_final: 0.8787 (p0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0762 time to fit residues: 11.6413 Evaluate side-chains 91 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 22 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.037272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.026589 restraints weight = 39008.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.028101 restraints weight = 21634.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.029231 restraints weight = 14541.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.030056 restraints weight = 10774.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.030697 restraints weight = 8561.322| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 5147 Z= 0.124 Angle : 0.717 22.047 7016 Z= 0.358 Chirality : 0.048 0.263 758 Planarity : 0.005 0.057 907 Dihedral : 5.307 30.151 710 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.02 % Favored : 89.83 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: -2.94 (0.32), residues: 639 helix: -3.11 (0.77), residues: 33 sheet: -1.58 (0.34), residues: 194 loop : -2.13 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 98 TYR 0.015 0.001 TYR C 85 PHE 0.036 0.001 PHE A 456 TRP 0.023 0.001 TRP D 47 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5140) covalent geometry : angle 0.71438 ( 7004) SS BOND : bond 0.00486 ( 6) SS BOND : angle 1.73800 ( 12) hydrogen bonds : bond 0.03214 ( 98) hydrogen bonds : angle 6.00200 ( 243) Misc. bond : bond 0.00905 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.222 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 338 PHE cc_start: 0.8438 (t80) cc_final: 0.8082 (t80) REVERT: A 396 TYR cc_start: 0.8740 (m-10) cc_final: 0.8408 (m-80) REVERT: B 72 SER cc_start: 0.9495 (t) cc_final: 0.9280 (p) REVERT: B 103 TYR cc_start: 0.8704 (p90) cc_final: 0.8186 (p90) REVERT: B 108 PHE cc_start: 0.8889 (m-80) cc_final: 0.7714 (m-80) REVERT: B 110 PHE cc_start: 0.9314 (m-80) cc_final: 0.8544 (m-80) REVERT: B 111 ASP cc_start: 0.9305 (t0) cc_final: 0.8327 (m-30) REVERT: C 35 TYR cc_start: 0.8902 (m-80) cc_final: 0.7810 (m-80) REVERT: C 49 TYR cc_start: 0.9361 (m-80) cc_final: 0.8940 (m-80) REVERT: D 34 ILE cc_start: 0.9648 (mm) cc_final: 0.9405 (tp) REVERT: D 51 ASN cc_start: 0.9562 (t0) cc_final: 0.9341 (t0) REVERT: D 71 THR cc_start: 0.9293 (p) cc_final: 0.8980 (p) REVERT: D 80 TYR cc_start: 0.9218 (m-80) cc_final: 0.8855 (m-80) REVERT: D 81 MET cc_start: 0.9157 (mmp) cc_final: 0.8564 (mmm) REVERT: D 83 LEU cc_start: 0.9392 (tp) cc_final: 0.9125 (tp) REVERT: E 4 MET cc_start: 0.7841 (tpp) cc_final: 0.7312 (tpp) REVERT: E 31 ASN cc_start: 0.9386 (p0) cc_final: 0.9062 (p0) REVERT: E 34 ASN cc_start: 0.8905 (m-40) cc_final: 0.8053 (m110) REVERT: E 93 ASP cc_start: 0.8898 (p0) cc_final: 0.8514 (p0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0829 time to fit residues: 12.8039 Evaluate side-chains 92 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.0040 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** 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 = 0.2851 r_free = 0.2851 target = 0.036619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.026210 restraints weight = 39215.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.027683 restraints weight = 22342.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.028785 restraints weight = 15185.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.029527 restraints weight = 11370.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.030172 restraints weight = 9226.282| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5147 Z= 0.137 Angle : 0.706 10.914 7016 Z= 0.365 Chirality : 0.048 0.247 758 Planarity : 0.005 0.061 907 Dihedral : 5.295 24.178 710 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.02 % Favored : 89.83 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -2.93 (0.32), residues: 639 helix: -3.06 (0.78), residues: 33 sheet: -1.55 (0.34), residues: 199 loop : -2.14 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 98 TYR 0.017 0.001 TYR C 85 PHE 0.019 0.001 PHE A 456 TRP 0.027 0.002 TRP D 47 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5140) covalent geometry : angle 0.70297 ( 7004) SS BOND : bond 0.00431 ( 6) SS BOND : angle 1.81286 ( 12) hydrogen bonds : bond 0.03502 ( 98) hydrogen bonds : angle 6.02322 ( 243) Misc. bond : bond 0.00364 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.217 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 338 PHE cc_start: 0.8425 (t80) cc_final: 0.8085 (t80) REVERT: A 396 TYR cc_start: 0.8761 (m-10) cc_final: 0.8422 (m-80) REVERT: A 462 LYS cc_start: 0.9163 (tmmt) cc_final: 0.8939 (tmtt) REVERT: A 465 GLU cc_start: 0.8160 (pt0) cc_final: 0.7886 (pt0) REVERT: B 72 SER cc_start: 0.9498 (t) cc_final: 0.9279 (p) REVERT: B 103 TYR cc_start: 0.8720 (p90) cc_final: 0.8193 (p90) REVERT: B 108 PHE cc_start: 0.8943 (m-80) cc_final: 0.7908 (m-80) REVERT: B 110 PHE cc_start: 0.9332 (m-80) cc_final: 0.8571 (m-80) REVERT: B 111 ASP cc_start: 0.9323 (t0) cc_final: 0.8316 (m-30) REVERT: C 35 TYR cc_start: 0.8862 (m-80) cc_final: 0.7773 (m-80) REVERT: C 49 TYR cc_start: 0.9393 (m-80) cc_final: 0.8974 (m-80) REVERT: D 34 ILE cc_start: 0.9621 (mm) cc_final: 0.9383 (tp) REVERT: D 51 ASN cc_start: 0.9573 (t0) cc_final: 0.9242 (t0) REVERT: D 81 MET cc_start: 0.9076 (mmp) cc_final: 0.8671 (mmm) REVERT: E 11 LEU cc_start: 0.9033 (mm) cc_final: 0.8702 (mm) REVERT: E 50 ASP cc_start: 0.9673 (m-30) cc_final: 0.9351 (t0) REVERT: E 70 ASP cc_start: 0.9382 (m-30) cc_final: 0.9126 (t0) REVERT: E 71 PHE cc_start: 0.8540 (m-10) cc_final: 0.8338 (m-10) REVERT: E 93 ASP cc_start: 0.8852 (p0) cc_final: 0.8525 (p0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0816 time to fit residues: 12.0539 Evaluate side-chains 92 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 3 optimal weight: 0.0570 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 overall best weight: 0.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** 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 = 0.2872 r_free = 0.2872 target = 0.037278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.026753 restraints weight = 40043.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.028265 restraints weight = 22355.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.029368 restraints weight = 15071.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.030184 restraints weight = 11222.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.030797 restraints weight = 8952.848| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5147 Z= 0.128 Angle : 0.698 16.896 7016 Z= 0.354 Chirality : 0.048 0.255 758 Planarity : 0.005 0.063 907 Dihedral : 5.250 24.290 710 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.33 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -2.91 (0.32), residues: 639 helix: -3.06 (0.79), residues: 33 sheet: -1.55 (0.34), residues: 195 loop : -2.11 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 457 TYR 0.011 0.001 TYR C 85 PHE 0.065 0.002 PHE A 456 TRP 0.026 0.002 TRP B 36 HIS 0.002 0.001 HIS C 33 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5140) covalent geometry : angle 0.69583 ( 7004) SS BOND : bond 0.00553 ( 6) SS BOND : angle 1.55151 ( 12) hydrogen bonds : bond 0.03166 ( 98) hydrogen bonds : angle 5.85253 ( 243) Misc. bond : bond 0.00908 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.211 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 338 PHE cc_start: 0.8360 (t80) cc_final: 0.8017 (t80) REVERT: A 396 TYR cc_start: 0.8718 (m-10) cc_final: 0.8385 (m-80) REVERT: B 52 TYR cc_start: 0.9732 (p90) cc_final: 0.9051 (p90) REVERT: B 57 TRP cc_start: 0.9572 (m-90) cc_final: 0.9313 (m-90) REVERT: B 72 SER cc_start: 0.9507 (t) cc_final: 0.9288 (p) REVERT: B 103 TYR cc_start: 0.8652 (p90) cc_final: 0.8144 (p90) REVERT: B 108 PHE cc_start: 0.8951 (m-80) cc_final: 0.7880 (m-80) REVERT: B 110 PHE cc_start: 0.9353 (m-80) cc_final: 0.8569 (m-80) REVERT: B 111 ASP cc_start: 0.9346 (t0) cc_final: 0.8346 (m-30) REVERT: C 35 TYR cc_start: 0.8899 (m-80) cc_final: 0.7854 (m-80) REVERT: C 49 TYR cc_start: 0.9403 (m-80) cc_final: 0.8958 (m-80) REVERT: D 34 ILE cc_start: 0.9615 (mm) cc_final: 0.9319 (tp) REVERT: D 51 ASN cc_start: 0.9631 (t0) cc_final: 0.9281 (t0) REVERT: D 71 THR cc_start: 0.9292 (p) cc_final: 0.8968 (p) REVERT: D 80 TYR cc_start: 0.9193 (m-80) cc_final: 0.8862 (m-80) REVERT: D 81 MET cc_start: 0.9246 (mmp) cc_final: 0.8693 (mmm) REVERT: D 83 LEU cc_start: 0.9391 (tp) cc_final: 0.9145 (tp) REVERT: E 29 ILE cc_start: 0.9003 (pt) cc_final: 0.8764 (pt) REVERT: E 93 ASP cc_start: 0.8989 (p0) cc_final: 0.8643 (p0) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0664 time to fit residues: 10.2437 Evaluate side-chains 96 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 7.9990 chunk 14 optimal weight: 0.0570 chunk 1 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN D 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.035750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.025265 restraints weight = 40392.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.026717 restraints weight = 22885.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.027772 restraints weight = 15530.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.028546 restraints weight = 11644.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.029112 restraints weight = 9341.073| |-----------------------------------------------------------------------------| r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5147 Z= 0.160 Angle : 0.694 14.886 7016 Z= 0.356 Chirality : 0.048 0.255 758 Planarity : 0.005 0.060 907 Dihedral : 5.466 30.238 710 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.64 % Favored : 89.20 % Rotamer: Outliers : 0.18 % Allowed : 0.36 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: -3.00 (0.32), residues: 639 helix: -2.89 (0.81), residues: 33 sheet: -1.57 (0.34), residues: 201 loop : -2.22 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 76 TYR 0.031 0.002 TYR C 85 PHE 0.052 0.002 PHE A 456 TRP 0.030 0.002 TRP D 47 HIS 0.003 0.001 HIS C 33 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5140) covalent geometry : angle 0.69071 ( 7004) SS BOND : bond 0.00542 ( 6) SS BOND : angle 1.70331 ( 12) hydrogen bonds : bond 0.03382 ( 98) hydrogen bonds : angle 5.95221 ( 243) Misc. bond : bond 0.00929 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1100.13 seconds wall clock time: 19 minutes 47.91 seconds (1187.91 seconds total)