Starting phenix.real_space_refine on Tue Feb 11 13:21:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgi_37222/02_2025/8kgi_37222.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgi_37222/02_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_37222/02_2025/8kgi_37222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgi_37222/02_2025/8kgi_37222.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgi_37222/02_2025/8kgi_37222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgi_37222/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.20, per 1000 atoms: 0.73 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: 1.63 Conformation dependent library (CDL) restraints added in 913.3 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: 0.53 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: 1.65 Time building geometry restraints manager: 1.80 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: 1.340 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: 0.080 Process input model: 17.470 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.220 ------------------------------------------------------------------------------- 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 : 0.646 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: 0.1746 time to fit residues: 35.1021 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 : 0.657 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138729 restraints weight = 8437.017| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.27 r_work: 0.3579 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 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 : 0.615 Fit side-chains REVERT: A 60 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8157 (tm-30) REVERT: A 519 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8683 (mm) REVERT: B 60 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8157 (tm-30) REVERT: B 519 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8696 (mm) outliers start: 9 outliers final: 2 residues processed: 142 average time/residue: 0.1683 time to fit residues: 31.4872 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 : 0.604 ------------------------------------------------------------------------------- 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: 3.9990 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 0.0370 chunk 39 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 0.0470 overall best weight: 1.0160 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.186775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135340 restraints weight = 8472.134| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.23 r_work: 0.3533 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5916 Z= 0.271 Angle : 0.643 7.961 8070 Z= 0.313 Chirality : 0.046 0.305 980 Planarity : 0.004 0.031 986 Dihedral : 3.846 14.427 806 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.74 % Allowed : 15.07 % Favored : 82.19 % 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: 3.15 (0.32), residues: 766 helix: 2.67 (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 0.002 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 : 0.676 Fit side-chains REVERT: A 60 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8104 (tm-30) REVERT: B 60 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8105 (tm-30) REVERT: B 200 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: B 325 ASN cc_start: 0.7550 (t0) cc_final: 0.7341 (t0) outliers start: 16 outliers final: 9 residues processed: 149 average time/residue: 0.1619 time to fit residues: 32.0323 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 : 0.617 ------------------------------------------------------------------------------- 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: 0.9980 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 0.0770 chunk 71 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.4279 r_free = 0.4279 target = 0.188876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137769 restraints weight = 8645.551| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.28 r_work: 0.3570 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5916 Z= 0.184 Angle : 0.613 6.974 8070 Z= 0.299 Chirality : 0.043 0.272 980 Planarity : 0.004 0.030 986 Dihedral : 3.758 14.634 806 Min Nonbonded Distance : 2.427 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: 3.24 (0.32), residues: 766 helix: 2.76 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -0.44 (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 0.014 0.001 TYR A 90 ARG 0.002 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 168 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.608 Fit side-chains REVERT: A 60 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 378 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8385 (tt) REVERT: B 60 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 177 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8214 (tp40) REVERT: B 200 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: B 378 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8402 (tt) outliers start: 15 outliers final: 7 residues processed: 159 average time/residue: 0.1633 time to fit residues: 34.3190 Evaluate side-chains 152 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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: 8.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.189924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138274 restraints weight = 8504.493| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.21 r_work: 0.3550 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1786 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= 0.230 Angle : 0.628 6.421 8070 Z= 0.309 Chirality : 0.043 0.212 980 Planarity : 0.004 0.030 986 Dihedral : 3.850 18.996 806 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.74 % Allowed : 21.23 % 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: 2.72 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -0.49 (0.57), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 257 HIS 0.001 0.000 HIS A 533 PHE 0.019 0.001 PHE B 366 TYR 0.012 0.001 TYR B 90 ARG 0.003 0.000 ARG B 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: 16 poor density : 149 time to evaluate : 0.581 Fit side-chains REVERT: A 60 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 378 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8404 (tt) REVERT: B 60 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 200 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: B 378 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8392 (tt) outliers start: 16 outliers final: 11 residues processed: 157 average time/residue: 0.1584 time to fit residues: 32.8856 Evaluate side-chains 154 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 540 VAL 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: 7.9990 chunk 3 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.185987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134641 restraints weight = 8395.343| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.24 r_work: 0.3508 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5916 Z= 0.290 Angle : 0.678 6.887 8070 Z= 0.329 Chirality : 0.045 0.233 980 Planarity : 0.004 0.031 986 Dihedral : 3.943 18.020 806 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.08 % Allowed : 22.09 % Favored : 74.83 % 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: 3.10 (0.32), residues: 766 helix: 2.64 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.41 (0.59), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 257 HIS 0.001 0.001 HIS B 533 PHE 0.018 0.001 PHE A 198 TYR 0.014 0.001 TYR A 90 ARG 0.005 0.001 ARG B 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 160 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.716 Fit side-chains REVERT: A 60 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 378 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8431 (tt) REVERT: B 60 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8102 (tm-30) REVERT: B 200 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: B 378 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8419 (tt) outliers start: 18 outliers final: 11 residues processed: 150 average time/residue: 0.1621 time to fit residues: 32.2553 Evaluate side-chains 152 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 327 LEU 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 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 371 VAL Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 177 GLN B 350 ASN B 372 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.187515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136110 restraints weight = 8522.036| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.30 r_work: 0.3533 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 5916 Z= 0.234 Angle : 0.657 6.849 8070 Z= 0.319 Chirality : 0.045 0.276 980 Planarity : 0.004 0.031 986 Dihedral : 3.859 18.325 806 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.91 % Allowed : 22.26 % Favored : 74.83 % 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: 2.69 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.40 (0.59), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 257 HIS 0.001 0.001 HIS B 533 PHE 0.021 0.001 PHE B 366 TYR 0.009 0.001 TYR A 90 ARG 0.004 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 160 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.601 Fit side-chains REVERT: A 60 GLU cc_start: 0.8681 (tm-30) cc_final: 0.7886 (tp30) REVERT: A 378 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8411 (tt) REVERT: B 60 GLU cc_start: 0.8681 (tm-30) cc_final: 0.7892 (tp30) REVERT: B 200 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: B 378 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8400 (tt) outliers start: 17 outliers final: 9 residues processed: 153 average time/residue: 0.1687 time to fit residues: 34.4912 Evaluate side-chains 151 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 216 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 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** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.187385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.136769 restraints weight = 8389.888| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.24 r_work: 0.3539 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5916 Z= 0.230 Angle : 0.669 7.292 8070 Z= 0.325 Chirality : 0.045 0.250 980 Planarity : 0.004 0.031 986 Dihedral : 3.863 18.426 806 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.08 % Allowed : 22.95 % Favored : 73.97 % 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: 3.14 (0.32), residues: 766 helix: 2.66 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.37 (0.59), 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 0.018 0.001 PHE B 348 TYR 0.008 0.001 TYR A 90 ARG 0.003 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 161 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.661 Fit side-chains REVERT: A 60 GLU cc_start: 0.8677 (tm-30) cc_final: 0.7909 (tp30) REVERT: A 378 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8428 (tt) REVERT: A 536 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7046 (mt) REVERT: B 60 GLU cc_start: 0.8673 (tm-30) cc_final: 0.7916 (tp30) REVERT: B 200 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: B 378 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8410 (tt) REVERT: B 389 ARG cc_start: 0.6485 (mmt180) cc_final: 0.6066 (mmt-90) outliers start: 18 outliers final: 10 residues processed: 153 average time/residue: 0.1590 time to fit residues: 32.2181 Evaluate side-chains 155 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 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 216 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 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 = 0.4262 r_free = 0.4262 target = 0.186805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.135761 restraints weight = 8465.206| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.25 r_work: 0.3527 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2287 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= 0.251 Angle : 0.686 8.034 8070 Z= 0.333 Chirality : 0.045 0.232 980 Planarity : 0.004 0.031 986 Dihedral : 3.877 18.347 806 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.91 % Allowed : 23.29 % Favored : 73.80 % 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: 2.60 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -0.39 (0.60), residues: 154 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 0.020 0.001 PHE B 366 TYR 0.008 0.001 TYR A 90 ARG 0.003 0.000 ARG B 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 161 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 378 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8430 (tt) REVERT: A 536 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7057 (mt) REVERT: B 60 GLU cc_start: 0.8689 (tm-30) cc_final: 0.7926 (tp30) REVERT: B 200 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: B 378 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8402 (tt) REVERT: B 389 ARG cc_start: 0.6436 (mmt180) cc_final: 0.6015 (mmt-90) outliers start: 17 outliers final: 10 residues processed: 155 average time/residue: 0.1592 time to fit residues: 32.8768 Evaluate side-chains 157 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 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 216 VAL 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: 0.7980 chunk 54 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN ** B 177 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 = 0.4271 r_free = 0.4271 target = 0.187803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136850 restraints weight = 8590.008| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.28 r_work: 0.3543 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5916 Z= 0.231 Angle : 0.694 8.520 8070 Z= 0.337 Chirality : 0.045 0.219 980 Planarity : 0.004 0.031 986 Dihedral : 3.854 18.124 806 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: 3.07 (0.32), residues: 766 helix: 2.56 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -0.24 (0.60), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 257 HIS 0.001 0.000 HIS A 533 PHE 0.017 0.001 PHE B 198 TYR 0.008 0.001 TYR A 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 158 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8679 (tm-30) cc_final: 0.7932 (tp30) REVERT: A 378 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8430 (tt) REVERT: A 536 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6983 (mt) REVERT: B 60 GLU cc_start: 0.8678 (tm-30) cc_final: 0.7947 (tp30) REVERT: B 200 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: B 378 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8410 (tt) REVERT: B 389 ARG cc_start: 0.6318 (mmt180) cc_final: 0.5919 (mmt-90) REVERT: B 536 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.7057 (mt) outliers start: 16 outliers final: 10 residues processed: 152 average time/residue: 0.1586 time to fit residues: 31.8715 Evaluate side-chains 156 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 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 216 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 536 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN 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 = 0.188967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.137789 restraints weight = 8571.126| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.27 r_work: 0.3544 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5916 Z= 0.228 Angle : 0.690 7.577 8070 Z= 0.337 Chirality : 0.045 0.210 980 Planarity : 0.004 0.031 986 Dihedral : 3.834 17.934 806 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.74 % Allowed : 24.66 % Favored : 72.60 % 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: 3.00 (0.32), residues: 766 helix: 2.54 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -0.38 (0.59), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 257 HIS 0.001 0.000 HIS A 533 PHE 0.020 0.001 PHE B 366 TYR 0.008 0.001 TYR A 90 ARG 0.003 0.000 ARG B 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3262.70 seconds wall clock time: 58 minutes 28.46 seconds (3508.46 seconds total)