Starting phenix.real_space_refine on Thu Mar 6 10:04:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgi_37222/03_2025/8kgi_37222.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgi_37222/03_2025/8kgi_37222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kgi_37222/03_2025/8kgi_37222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgi_37222/03_2025/8kgi_37222.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgi_37222/03_2025/8kgi_37222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgi_37222/03_2025/8kgi_37222.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.048 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 32 5.16 5 C 3890 2.51 5 N 880 2.21 5 O 964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5766 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 2883 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 2883 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 93 Time building chain proxies: 4.76, per 1000 atoms: 0.83 Number of scatterers: 5766 At special positions: 0 Unit cell: (79.22, 103.452, 73.628, 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 32 16.00 O 964 8.00 N 880 7.00 C 3890 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.67 Conformation dependent library (CDL) restraints added in 945.4 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 85.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 removed outlier: 3.713A pdb=" N GLY A 29 " --> pdb=" O SER A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 30 through 55 removed outlier: 4.310A pdb=" N PHE A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 66 through 91 removed outlier: 4.419A pdb=" N SER A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 114 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.647A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 198 Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.524A pdb=" N SER A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.176A pdb=" N GLN A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 256 through 273 removed outlier: 3.876A pdb=" N GLY A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 310 through 324 Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 325 through 358 Processing helix chain 'A' and resid 363 through 390 Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 396 through 412 Processing helix chain 'A' and resid 412 through 420 removed outlier: 3.541A pdb=" N MET A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 544 removed outlier: 4.383A pdb=" N ASN A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Proline residue: A 535 - end of helix removed outlier: 3.818A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 548 through 566 Processing helix chain 'B' and resid 26 through 29 removed outlier: 3.713A pdb=" N GLY B 29 " --> pdb=" O SER B 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 29' Processing helix chain 'B' and resid 30 through 55 removed outlier: 4.315A pdb=" N PHE B 34 " --> pdb=" O ASN B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 63 Processing helix chain 'B' and resid 66 through 91 removed outlier: 4.417A pdb=" N SER B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 114 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 168 through 184 removed outlier: 3.645A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.502A pdb=" N SER B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 231 removed outlier: 4.173A pdb=" N GLN B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 256 through 273 removed outlier: 3.876A pdb=" N GLY B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 310 through 324 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 325 through 358 Processing helix chain 'B' and resid 363 through 390 Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 396 through 412 Processing helix chain 'B' and resid 412 through 420 removed outlier: 3.540A pdb=" N MET B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 544 removed outlier: 4.387A pdb=" N ASN B 534 " --> pdb=" O CYS B 530 " (cutoff:3.500A) Proline residue: B 535 - end of helix removed outlier: 3.817A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 547 No H-bonds generated for 'chain 'B' and resid 545 through 547' Processing helix chain 'B' and resid 548 through 566 450 hydrogen bonds defined for protein. 1338 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: 1.75 Time building geometry restraints manager: 1.88 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: 1672 1.34 - 1.46: 939 1.46 - 1.57: 3253 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 5916 Sorted by residual: bond pdb=" CB VAL A 540 " pdb=" CG2 VAL A 540 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.23e+00 bond pdb=" CB VAL B 540 " pdb=" CG2 VAL B 540 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CG LEU B 211 " pdb=" CD1 LEU B 211 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.90e-01 bond pdb=" CG LEU A 211 " pdb=" CD1 LEU A 211 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.85e-01 bond pdb=" CB GLN B 335 " pdb=" CG GLN B 335 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.69e-01 ... (remaining 5911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 7638 1.21 - 2.42: 311 2.42 - 3.63: 70 3.63 - 4.83: 27 4.83 - 6.04: 24 Bond angle restraints: 8070 Sorted by residual: angle pdb=" C MET A 538 " pdb=" N MET A 539 " pdb=" CA MET A 539 " ideal model delta sigma weight residual 120.31 116.65 3.66 1.52e+00 4.33e-01 5.81e+00 angle pdb=" C MET B 538 " pdb=" N MET B 539 " pdb=" CA MET B 539 " ideal model delta sigma weight residual 120.31 116.67 3.64 1.52e+00 4.33e-01 5.72e+00 angle pdb=" C VAL A 239 " pdb=" N ASN A 240 " pdb=" CA ASN A 240 " ideal model delta sigma weight residual 121.54 125.74 -4.20 1.91e+00 2.74e-01 4.84e+00 angle pdb=" C VAL B 239 " pdb=" N ASN B 240 " pdb=" CA ASN B 240 " ideal model delta sigma weight residual 121.54 125.73 -4.19 1.91e+00 2.74e-01 4.81e+00 angle pdb=" N ASN B 534 " pdb=" CA ASN B 534 " pdb=" C ASN B 534 " ideal model delta sigma weight residual 109.81 114.57 -4.76 2.21e+00 2.05e-01 4.65e+00 ... (remaining 8065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 3061 15.67 - 31.35: 248 31.35 - 47.02: 72 47.02 - 62.70: 11 62.70 - 78.37: 10 Dihedral angle restraints: 3402 sinusoidal: 1154 harmonic: 2248 Sorted by residual: dihedral pdb=" CB MET A 418 " pdb=" CG MET A 418 " pdb=" SD MET A 418 " pdb=" CE MET A 418 " ideal model delta sinusoidal sigma weight residual -60.00 -113.12 53.12 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" CB MET B 418 " pdb=" CG MET B 418 " pdb=" SD MET B 418 " pdb=" CE MET B 418 " ideal model delta sinusoidal sigma weight residual -60.00 -113.04 53.04 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CG LYS A 549 " pdb=" CD LYS A 549 " pdb=" CE LYS A 549 " pdb=" NZ LYS A 549 " ideal model delta sinusoidal sigma weight residual -180.00 -130.06 -49.94 3 1.50e+01 4.44e-03 8.84e+00 ... (remaining 3399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 591 0.032 - 0.064: 239 0.064 - 0.095: 116 0.095 - 0.127: 32 0.127 - 0.159: 2 Chirality restraints: 980 Sorted by residual: chirality pdb=" CB THR A 403 " pdb=" CA THR A 403 " pdb=" OG1 THR A 403 " pdb=" CG2 THR A 403 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CB THR B 403 " pdb=" CA THR B 403 " pdb=" OG1 THR B 403 " pdb=" CG2 THR B 403 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA SER A 568 " pdb=" N SER A 568 " pdb=" C SER A 568 " pdb=" CB SER A 568 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 977 not shown) Planarity restraints: 986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 311 " 0.010 2.00e-02 2.50e+03 9.37e-03 1.54e+00 pdb=" CG PHE B 311 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE B 311 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 311 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 311 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 311 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 311 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 311 " -0.010 2.00e-02 2.50e+03 9.09e-03 1.45e+00 pdb=" CG PHE A 311 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 311 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 311 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 311 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 311 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 311 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 413 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 414 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 414 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 414 " -0.016 5.00e-02 4.00e+02 ... (remaining 983 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1755 2.82 - 3.34: 6423 3.34 - 3.86: 9649 3.86 - 4.38: 10123 4.38 - 4.90: 18141 Nonbonded interactions: 46091 Sorted by model distance: nonbonded pdb=" OH TYR B 194 " pdb=" O PRO B 279 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR A 194 " pdb=" O PRO A 279 " model vdw 2.308 3.040 nonbonded pdb=" OG SER A 393 " pdb=" N LEU A 394 " model vdw 2.318 3.120 nonbonded pdb=" OG SER B 393 " pdb=" N LEU B 394 " model vdw 2.318 3.120 nonbonded pdb=" NH1 ARG A 97 " pdb=" OG SER A 193 " model vdw 2.342 3.120 ... (remaining 46086 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.430 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 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 0.037 5916 Z= 0.211 Angle : 0.668 6.042 8070 Z= 0.339 Chirality : 0.043 0.159 980 Planarity : 0.004 0.029 986 Dihedral : 13.818 78.370 1950 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.32), residues: 766 helix: 2.49 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -0.84 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 257 HIS 0.001 0.000 HIS A 119 PHE 0.021 0.001 PHE B 311 TYR 0.015 0.002 TYR B 90 ARG 0.002 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.631 Fit side-chains REVERT: B 125 TYR cc_start: 0.6453 (t80) cc_final: 0.6029 (t80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1586 time to fit residues: 31.9040 Evaluate side-chains 129 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.189791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138779 restraints weight = 8437.017| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.25 r_work: 0.3584 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5916 Z= 0.239 Angle : 0.647 7.417 8070 Z= 0.313 Chirality : 0.044 0.312 980 Planarity : 0.004 0.031 986 Dihedral : 3.773 14.291 806 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.54 % Allowed : 11.30 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.32), residues: 766 helix: 2.64 (0.21), residues: 606 sheet: None (None), residues: 0 loop : -0.44 (0.57), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 257 HIS 0.001 0.001 HIS B 533 PHE 0.023 0.001 PHE B 348 TYR 0.014 0.001 TYR A 537 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.627 Fit side-chains REVERT: A 60 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8154 (tm-30) REVERT: A 519 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8690 (mm) REVERT: B 60 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8156 (tm-30) REVERT: B 519 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8700 (mm) outliers start: 9 outliers final: 2 residues processed: 142 average time/residue: 0.1591 time to fit residues: 29.9203 Evaluate side-chains 133 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 519 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.0470 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.186980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135135 restraints weight = 8495.137| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.31 r_work: 0.3536 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5916 Z= 0.268 Angle : 0.644 7.906 8070 Z= 0.314 Chirality : 0.046 0.307 980 Planarity : 0.004 0.031 986 Dihedral : 3.846 14.381 806 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.74 % Allowed : 15.24 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.32), residues: 766 helix: 2.68 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -0.34 (0.58), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 257 HIS 0.001 0.000 HIS B 533 PHE 0.020 0.001 PHE B 348 TYR 0.015 0.002 TYR A 90 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.130 Fit side-chains REVERT: A 60 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8105 (tm-30) REVERT: B 60 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 200 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: B 325 ASN cc_start: 0.7552 (t0) cc_final: 0.7342 (t0) outliers start: 16 outliers final: 9 residues processed: 148 average time/residue: 0.2009 time to fit residues: 40.2221 Evaluate side-chains 140 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 57 optimal weight: 0.4980 chunk 61 optimal weight: 0.4980 chunk 71 optimal weight: 0.0060 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.189860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.138735 restraints weight = 8651.065| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.36 r_work: 0.3561 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5916 Z= 0.183 Angle : 0.615 7.197 8070 Z= 0.300 Chirality : 0.043 0.275 980 Planarity : 0.004 0.030 986 Dihedral : 3.756 14.607 806 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.57 % Allowed : 18.15 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.32), residues: 766 helix: 2.77 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -0.43 (0.57), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 257 HIS 0.001 0.000 HIS B 533 PHE 0.020 0.001 PHE B 348 TYR 0.013 0.001 TYR B 90 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.656 Fit side-chains REVERT: A 60 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8052 (tm-30) REVERT: A 378 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8376 (tt) REVERT: B 60 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 200 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: B 378 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8388 (tt) outliers start: 15 outliers final: 7 residues processed: 155 average time/residue: 0.1578 time to fit residues: 32.5068 Evaluate side-chains 151 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.187677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.136081 restraints weight = 8503.321| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.24 r_work: 0.3546 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5916 Z= 0.231 Angle : 0.631 6.477 8070 Z= 0.310 Chirality : 0.043 0.201 980 Planarity : 0.004 0.033 986 Dihedral : 3.868 19.204 806 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.57 % Allowed : 21.40 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.32), residues: 766 helix: 2.73 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -0.48 (0.57), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 257 HIS 0.001 0.000 HIS A 533 PHE 0.019 0.001 PHE A 366 TYR 0.013 0.001 TYR B 90 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.833 Fit side-chains REVERT: A 60 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 378 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8401 (tt) REVERT: B 60 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8036 (tm-30) REVERT: B 200 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: B 378 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8394 (tt) outliers start: 15 outliers final: 9 residues processed: 158 average time/residue: 0.1698 time to fit residues: 36.3027 Evaluate side-chains 153 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN B 77 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.187514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136224 restraints weight = 8380.903| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.25 r_work: 0.3537 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5916 Z= 0.246 Angle : 0.660 6.809 8070 Z= 0.320 Chirality : 0.044 0.196 980 Planarity : 0.004 0.034 986 Dihedral : 3.871 17.461 806 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.57 % Allowed : 22.77 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.32), residues: 766 helix: 2.69 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.45 (0.58), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 257 HIS 0.001 0.000 HIS B 533 PHE 0.017 0.001 PHE B 348 TYR 0.008 0.001 TYR A 90 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.669 Fit side-chains REVERT: A 60 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 378 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8402 (tt) REVERT: B 60 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8010 (tm-30) REVERT: B 200 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: B 378 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8394 (tt) outliers start: 15 outliers final: 9 residues processed: 154 average time/residue: 0.1985 time to fit residues: 41.4500 Evaluate side-chains 150 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.0010 chunk 35 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.0470 chunk 38 optimal weight: 0.0070 chunk 28 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 overall best weight: 0.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN B 350 ASN B 372 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.191023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139637 restraints weight = 8491.883| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.36 r_work: 0.3573 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5916 Z= 0.179 Angle : 0.643 7.188 8070 Z= 0.311 Chirality : 0.043 0.204 980 Planarity : 0.004 0.030 986 Dihedral : 3.737 17.948 806 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.23 % Allowed : 22.77 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.32), residues: 766 helix: 2.71 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.48 (0.57), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 257 HIS 0.001 0.000 HIS A 533 PHE 0.022 0.001 PHE B 366 TYR 0.008 0.001 TYR B 90 ARG 0.002 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.627 Fit side-chains REVERT: A 60 GLU cc_start: 0.8676 (tm-30) cc_final: 0.7925 (tp30) REVERT: A 378 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8387 (tt) REVERT: B 60 GLU cc_start: 0.8679 (tm-30) cc_final: 0.7930 (tp30) REVERT: B 200 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: B 378 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8383 (tt) outliers start: 13 outliers final: 7 residues processed: 158 average time/residue: 0.1554 time to fit residues: 32.9591 Evaluate side-chains 153 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.0170 chunk 40 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.188993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138209 restraints weight = 8409.979| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.29 r_work: 0.3555 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5916 Z= 0.216 Angle : 0.671 7.402 8070 Z= 0.325 Chirality : 0.044 0.179 980 Planarity : 0.004 0.030 986 Dihedral : 3.769 17.935 806 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.23 % Allowed : 23.29 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.32), residues: 766 helix: 2.67 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.48 (0.57), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 257 HIS 0.001 0.000 HIS B 119 PHE 0.021 0.001 PHE A 198 TYR 0.014 0.001 TYR B 194 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.627 Fit side-chains REVERT: A 60 GLU cc_start: 0.8680 (tm-30) cc_final: 0.7930 (tp30) REVERT: A 378 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8425 (tt) REVERT: A 536 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7038 (mt) REVERT: B 60 GLU cc_start: 0.8688 (tm-30) cc_final: 0.7950 (tp30) REVERT: B 200 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: B 378 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8418 (tt) outliers start: 13 outliers final: 8 residues processed: 150 average time/residue: 0.1561 time to fit residues: 31.3003 Evaluate side-chains 149 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.188273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.137388 restraints weight = 8441.233| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.27 r_work: 0.3542 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5916 Z= 0.243 Angle : 0.685 8.373 8070 Z= 0.332 Chirality : 0.045 0.175 980 Planarity : 0.004 0.030 986 Dihedral : 3.797 17.956 806 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.74 % Allowed : 23.80 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.32), residues: 766 helix: 2.63 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.41 (0.57), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 257 HIS 0.001 0.000 HIS A 533 PHE 0.020 0.001 PHE A 366 TYR 0.010 0.001 TYR A 90 ARG 0.004 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.613 Fit side-chains REVERT: A 60 GLU cc_start: 0.8673 (tm-30) cc_final: 0.7904 (tp30) REVERT: A 378 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 536 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7066 (mt) REVERT: B 60 GLU cc_start: 0.8674 (tm-30) cc_final: 0.7913 (tp30) REVERT: B 200 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7839 (pm20) REVERT: B 378 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8401 (tt) outliers start: 16 outliers final: 8 residues processed: 152 average time/residue: 0.1568 time to fit residues: 31.8024 Evaluate side-chains 154 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 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 = 0.4268 r_free = 0.4268 target = 0.187630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136051 restraints weight = 8590.439| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.32 r_work: 0.3543 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5916 Z= 0.229 Angle : 0.696 8.374 8070 Z= 0.337 Chirality : 0.045 0.167 980 Planarity : 0.004 0.030 986 Dihedral : 3.826 17.798 806 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.40 % Allowed : 24.14 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.32), residues: 766 helix: 2.54 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -0.48 (0.58), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 257 HIS 0.001 0.000 HIS B 533 PHE 0.017 0.001 PHE B 348 TYR 0.009 0.001 TYR B 90 ARG 0.003 0.000 ARG B 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.631 Fit side-chains REVERT: A 60 GLU cc_start: 0.8696 (tm-30) cc_final: 0.7953 (tp30) REVERT: A 378 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8420 (tt) REVERT: B 60 GLU cc_start: 0.8690 (tm-30) cc_final: 0.7957 (tp30) REVERT: B 200 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7773 (pm20) REVERT: B 224 LEU cc_start: 0.7512 (tt) cc_final: 0.7055 (mp) REVERT: B 378 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8397 (tt) outliers start: 14 outliers final: 7 residues processed: 152 average time/residue: 0.1648 time to fit residues: 33.1491 Evaluate side-chains 146 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.189178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.138411 restraints weight = 8512.522| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.30 r_work: 0.3557 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5916 Z= 0.211 Angle : 0.691 8.184 8070 Z= 0.334 Chirality : 0.044 0.169 980 Planarity : 0.004 0.030 986 Dihedral : 3.785 17.680 806 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.05 % Allowed : 24.83 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.32), residues: 766 helix: 2.52 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -0.51 (0.58), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 257 HIS 0.001 0.000 HIS B 533 PHE 0.021 0.001 PHE A 366 TYR 0.009 0.001 TYR A 90 ARG 0.003 0.000 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3585.04 seconds wall clock time: 64 minutes 22.84 seconds (3862.84 seconds total)