Starting phenix.real_space_refine on Wed Jul 23 23:35:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jj3_61516/07_2025/9jj3_61516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jj3_61516/07_2025/9jj3_61516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jj3_61516/07_2025/9jj3_61516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jj3_61516/07_2025/9jj3_61516.map" model { file = "/net/cci-nas-00/data/ceres_data/9jj3_61516/07_2025/9jj3_61516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jj3_61516/07_2025/9jj3_61516.cif" } resolution = 3.03 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= -0.000 sd= 0.005 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 26 5.16 5 C 3004 2.51 5 N 752 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4586 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2293 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 5, 'TRANS': 285} Chain breaks: 1 Chain: "A" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2293 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 5, 'TRANS': 285} Chain breaks: 1 Time building chain proxies: 3.74, per 1000 atoms: 0.82 Number of scatterers: 4586 At special positions: 0 Unit cell: (53.95, 83.83, 100.43, 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 26 16.00 O 804 8.00 N 752 7.00 C 3004 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: 1.08 Conformation dependent library (CDL) restraints added in 513.8 milliseconds 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 70.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 101 through 135 removed outlier: 4.063A pdb=" N LEU B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 165 removed outlier: 3.705A pdb=" N MET B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU B 145 " --> pdb=" O MET B 141 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N HIS B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 206 removed outlier: 3.786A pdb=" N VAL B 181 " --> pdb=" O HIS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 236 removed outlier: 3.778A pdb=" N LEU B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 297 Processing helix chain 'B' and resid 303 through 332 removed outlier: 4.337A pdb=" N ILE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG B 322 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE B 323 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 350 Processing helix chain 'B' and resid 386 through 402 Processing helix chain 'A' and resid 101 through 135 removed outlier: 3.873A pdb=" N LEU A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 removed outlier: 3.721A pdb=" N MET A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 165 removed outlier: 4.265A pdb=" N HIS A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 206 removed outlier: 3.804A pdb=" N VAL A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 236 removed outlier: 3.853A pdb=" N LEU A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 297 Processing helix chain 'A' and resid 303 through 332 removed outlier: 4.556A pdb=" N ILE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 386 through 402 Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 366 removed outlier: 6.121A pdb=" N VAL B 357 " --> pdb=" O GLN B 377 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLN B 377 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP B 359 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER B 370 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N THR B 407 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ALA B 372 " --> pdb=" O THR B 407 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 357 removed outlier: 3.649A pdb=" N SER A 356 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 366 removed outlier: 7.013A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER A 370 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR A 407 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA A 372 " --> pdb=" O THR A 407 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 987 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: 1.17 Time building geometry restraints manager: 1.29 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: 1415 1.34 - 1.46: 668 1.46 - 1.57: 2539 1.57 - 1.69: 2 1.69 - 1.81: 46 Bond restraints: 4670 Sorted by residual: bond pdb=" CB PRO B 299 " pdb=" CG PRO B 299 " ideal model delta sigma weight residual 1.492 1.629 -0.137 5.00e-02 4.00e+02 7.51e+00 bond pdb=" CB PRO A 299 " pdb=" CG PRO A 299 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.77e+00 bond pdb=" CG PRO A 299 " pdb=" CD PRO A 299 " ideal model delta sigma weight residual 1.503 1.558 -0.055 3.40e-02 8.65e+02 2.62e+00 bond pdb=" CG PRO B 299 " pdb=" CD PRO B 299 " ideal model delta sigma weight residual 1.503 1.551 -0.048 3.40e-02 8.65e+02 1.97e+00 bond pdb=" CB ASN A 210 " pdb=" CG ASN A 210 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.46e+00 ... (remaining 4665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 6239 2.41 - 4.83: 76 4.83 - 7.24: 13 7.24 - 9.66: 4 9.66 - 12.07: 4 Bond angle restraints: 6336 Sorted by residual: angle pdb=" CA PRO B 299 " pdb=" N PRO B 299 " pdb=" CD PRO B 299 " ideal model delta sigma weight residual 112.00 101.38 10.62 1.40e+00 5.10e-01 5.75e+01 angle pdb=" CA PRO A 299 " pdb=" N PRO A 299 " pdb=" CD PRO A 299 " ideal model delta sigma weight residual 112.00 101.79 10.21 1.40e+00 5.10e-01 5.32e+01 angle pdb=" CA LYS A 298 " pdb=" CB LYS A 298 " pdb=" CG LYS A 298 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA MET A 209 " pdb=" CB MET A 209 " pdb=" CG MET A 209 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" C MET A 209 " pdb=" N ASN A 210 " pdb=" CA ASN A 210 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+01 ... (remaining 6331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.12: 2247 13.12 - 26.23: 327 26.23 - 39.35: 144 39.35 - 52.46: 49 52.46 - 65.57: 13 Dihedral angle restraints: 2780 sinusoidal: 1070 harmonic: 1710 Sorted by residual: dihedral pdb=" CA ASN A 210 " pdb=" C ASN A 210 " pdb=" N TYR A 211 " pdb=" CA TYR A 211 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASN B 210 " pdb=" C ASN B 210 " pdb=" N TYR B 211 " pdb=" CA TYR B 211 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASN A 281 " pdb=" CB ASN A 281 " pdb=" CG ASN A 281 " pdb=" OD1 ASN A 281 " ideal model delta sinusoidal sigma weight residual 120.00 -176.08 -63.92 2 2.00e+01 2.50e-03 9.68e+00 ... (remaining 2777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 562 0.039 - 0.078: 168 0.078 - 0.116: 33 0.116 - 0.155: 12 0.155 - 0.194: 5 Chirality restraints: 780 Sorted by residual: chirality pdb=" CB THR B 115 " pdb=" CA THR B 115 " pdb=" OG1 THR B 115 " pdb=" CG2 THR B 115 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CG LEU B 360 " pdb=" CB LEU B 360 " pdb=" CD1 LEU B 360 " pdb=" CD2 LEU B 360 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CB THR A 115 " pdb=" CA THR A 115 " pdb=" OG1 THR A 115 " pdb=" CG2 THR A 115 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.15e-01 ... (remaining 777 not shown) Planarity restraints: 762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 298 " -0.078 5.00e-02 4.00e+02 1.11e-01 1.99e+01 pdb=" N PRO B 299 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO B 299 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 299 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 298 " 0.076 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO A 299 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 360 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C LEU B 360 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU B 360 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 361 " -0.010 2.00e-02 2.50e+03 ... (remaining 759 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1005 2.78 - 3.31: 4809 3.31 - 3.84: 7671 3.84 - 4.37: 8288 4.37 - 4.90: 14298 Nonbonded interactions: 36071 Sorted by model distance: nonbonded pdb=" O TRP B 162 " pdb=" OG SER B 165 " model vdw 2.247 3.040 nonbonded pdb=" N GLU A 388 " pdb=" OE1 GLU A 388 " model vdw 2.249 3.120 nonbonded pdb=" N GLU B 388 " pdb=" OE1 GLU B 388 " model vdw 2.250 3.120 nonbonded pdb=" O TRP A 162 " pdb=" OG SER A 165 " model vdw 2.251 3.040 nonbonded pdb=" O MET B 209 " pdb=" ND2 ASN B 210 " model vdw 2.253 3.120 ... (remaining 36066 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: 0.02 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: 1.460 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 14.960 Find NCS groups from input model: 0.130 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 4670 Z= 0.154 Angle : 0.712 12.069 6336 Z= 0.377 Chirality : 0.042 0.194 780 Planarity : 0.006 0.111 762 Dihedral : 16.420 65.575 1672 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.20 % Allowed : 34.19 % Favored : 65.61 % 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: 2.17 (0.38), residues: 574 helix: 2.64 (0.26), residues: 382 sheet: -0.89 (0.78), residues: 52 loop : -1.12 (0.63), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.001 0.000 HIS A 146 PHE 0.014 0.001 PHE A 312 TYR 0.010 0.001 TYR B 404 ARG 0.002 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.13583 ( 329) hydrogen bonds : angle 4.84417 ( 987) covalent geometry : bond 0.00419 ( 4670) covalent geometry : angle 0.71194 ( 6336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.558 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.1047 time to fit residues: 16.6908 Evaluate side-chains 110 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 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 = 0.3489 r_free = 0.3489 target = 0.099216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078562 restraints weight = 9026.384| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.05 r_work: 0.2946 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4670 Z= 0.151 Angle : 0.590 8.318 6336 Z= 0.313 Chirality : 0.041 0.148 780 Planarity : 0.004 0.041 762 Dihedral : 4.108 17.909 624 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.34 % Allowed : 28.06 % Favored : 66.60 % 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: 2.31 (0.37), residues: 574 helix: 2.66 (0.25), residues: 386 sheet: -0.93 (0.79), residues: 52 loop : -0.86 (0.63), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 162 HIS 0.001 0.001 HIS B 146 PHE 0.014 0.001 PHE A 312 TYR 0.012 0.001 TYR A 404 ARG 0.002 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 329) hydrogen bonds : angle 3.75717 ( 987) covalent geometry : bond 0.00353 ( 4670) covalent geometry : angle 0.59042 ( 6336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.552 Fit side-chains REVERT: B 210 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8295 (p0) REVERT: B 285 SER cc_start: 0.8951 (m) cc_final: 0.8541 (t) REVERT: B 359 ASP cc_start: 0.7888 (t0) cc_final: 0.7688 (t0) REVERT: A 148 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8831 (mp) REVERT: A 189 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8485 (tt) REVERT: A 285 SER cc_start: 0.8940 (m) cc_final: 0.8531 (t) REVERT: A 302 LYS cc_start: 0.8971 (tptm) cc_final: 0.8652 (tptp) REVERT: A 359 ASP cc_start: 0.7976 (t0) cc_final: 0.7634 (t0) outliers start: 27 outliers final: 13 residues processed: 129 average time/residue: 0.1097 time to fit residues: 19.7094 Evaluate side-chains 123 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 406 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075867 restraints weight = 9093.081| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.06 r_work: 0.2925 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4670 Z= 0.167 Angle : 0.575 7.356 6336 Z= 0.308 Chirality : 0.041 0.141 780 Planarity : 0.003 0.038 762 Dihedral : 4.117 16.626 624 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.53 % Allowed : 27.67 % Favored : 66.80 % 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: 2.38 (0.37), residues: 574 helix: 2.68 (0.25), residues: 386 sheet: -0.88 (0.80), residues: 52 loop : -0.72 (0.64), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 162 HIS 0.002 0.000 HIS A 146 PHE 0.014 0.001 PHE A 312 TYR 0.013 0.001 TYR A 404 ARG 0.001 0.000 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.04473 ( 329) hydrogen bonds : angle 3.73500 ( 987) covalent geometry : bond 0.00386 ( 4670) covalent geometry : angle 0.57469 ( 6336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.510 Fit side-chains REVERT: B 189 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8510 (tt) REVERT: B 210 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8310 (p0) REVERT: B 285 SER cc_start: 0.8974 (m) cc_final: 0.8620 (t) REVERT: B 359 ASP cc_start: 0.8051 (t0) cc_final: 0.7587 (t0) REVERT: A 148 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8830 (mp) REVERT: A 189 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8521 (tt) REVERT: A 285 SER cc_start: 0.8954 (m) cc_final: 0.8582 (t) REVERT: A 302 LYS cc_start: 0.9027 (tptm) cc_final: 0.8766 (tptp) REVERT: A 359 ASP cc_start: 0.8110 (t0) cc_final: 0.7584 (t0) outliers start: 28 outliers final: 16 residues processed: 132 average time/residue: 0.1077 time to fit residues: 19.9725 Evaluate side-chains 125 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 406 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078385 restraints weight = 9064.945| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.02 r_work: 0.2978 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4670 Z= 0.138 Angle : 0.569 7.458 6336 Z= 0.302 Chirality : 0.040 0.141 780 Planarity : 0.003 0.043 762 Dihedral : 4.046 16.531 624 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.74 % Allowed : 29.45 % Favored : 65.81 % 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: 2.42 (0.37), residues: 574 helix: 2.76 (0.25), residues: 384 sheet: -0.97 (0.78), residues: 52 loop : -0.76 (0.63), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 162 HIS 0.009 0.001 HIS A 395 PHE 0.014 0.001 PHE A 312 TYR 0.012 0.001 TYR A 404 ARG 0.001 0.000 ARG B 405 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 329) hydrogen bonds : angle 3.63658 ( 987) covalent geometry : bond 0.00307 ( 4670) covalent geometry : angle 0.56859 ( 6336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: B 189 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8466 (tt) REVERT: B 210 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8123 (p0) REVERT: B 285 SER cc_start: 0.8961 (m) cc_final: 0.8585 (t) REVERT: B 302 LYS cc_start: 0.9059 (tptm) cc_final: 0.8796 (tptp) REVERT: B 359 ASP cc_start: 0.7917 (t0) cc_final: 0.7460 (t0) REVERT: A 189 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8472 (tt) REVERT: A 285 SER cc_start: 0.8945 (m) cc_final: 0.8579 (t) REVERT: A 359 ASP cc_start: 0.8072 (t0) cc_final: 0.7504 (t0) outliers start: 24 outliers final: 18 residues processed: 134 average time/residue: 0.1161 time to fit residues: 21.0335 Evaluate side-chains 129 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 406 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.0010 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.099144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.078897 restraints weight = 9139.621| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.99 r_work: 0.2982 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4670 Z= 0.135 Angle : 0.570 7.522 6336 Z= 0.306 Chirality : 0.041 0.160 780 Planarity : 0.003 0.043 762 Dihedral : 4.025 16.611 624 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 5.73 % Allowed : 29.45 % Favored : 64.82 % 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: 2.48 (0.37), residues: 574 helix: 2.80 (0.25), residues: 384 sheet: -1.03 (0.78), residues: 52 loop : -0.69 (0.63), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.007 0.001 HIS A 395 PHE 0.014 0.001 PHE A 312 TYR 0.013 0.001 TYR A 404 ARG 0.005 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 329) hydrogen bonds : angle 3.60788 ( 987) covalent geometry : bond 0.00298 ( 4670) covalent geometry : angle 0.56967 ( 6336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.537 Fit side-chains REVERT: B 189 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8488 (tt) REVERT: B 204 GLN cc_start: 0.7674 (tp40) cc_final: 0.7331 (mp10) REVERT: B 210 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8313 (p0) REVERT: B 285 SER cc_start: 0.8983 (m) cc_final: 0.8592 (t) REVERT: A 189 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8468 (tt) REVERT: A 285 SER cc_start: 0.8971 (m) cc_final: 0.8585 (t) REVERT: A 359 ASP cc_start: 0.8107 (t0) cc_final: 0.7502 (t0) REVERT: A 360 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8798 (tt) outliers start: 29 outliers final: 20 residues processed: 131 average time/residue: 0.1115 time to fit residues: 20.3842 Evaluate side-chains 135 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 406 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.077214 restraints weight = 9108.405| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.02 r_work: 0.2958 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4670 Z= 0.154 Angle : 0.579 7.330 6336 Z= 0.310 Chirality : 0.041 0.157 780 Planarity : 0.003 0.044 762 Dihedral : 4.049 16.719 624 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 6.52 % Allowed : 29.25 % Favored : 64.23 % 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: 2.45 (0.37), residues: 574 helix: 2.77 (0.25), residues: 384 sheet: -1.08 (0.78), residues: 52 loop : -0.64 (0.63), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.007 0.001 HIS A 395 PHE 0.013 0.001 PHE A 312 TYR 0.012 0.001 TYR A 404 ARG 0.006 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 329) hydrogen bonds : angle 3.62000 ( 987) covalent geometry : bond 0.00348 ( 4670) covalent geometry : angle 0.57938 ( 6336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.502 Fit side-chains REVERT: B 189 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8470 (tt) REVERT: B 210 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8093 (p0) REVERT: B 285 SER cc_start: 0.8952 (m) cc_final: 0.8577 (t) REVERT: A 189 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8443 (tt) REVERT: A 285 SER cc_start: 0.8953 (m) cc_final: 0.8584 (t) REVERT: A 302 LYS cc_start: 0.9121 (tptm) cc_final: 0.8794 (tptp) REVERT: A 359 ASP cc_start: 0.8096 (t0) cc_final: 0.7585 (t0) REVERT: A 360 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8841 (tt) outliers start: 33 outliers final: 27 residues processed: 132 average time/residue: 0.1082 time to fit residues: 19.9033 Evaluate side-chains 141 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.098744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078164 restraints weight = 9014.341| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.02 r_work: 0.2958 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4670 Z= 0.151 Angle : 0.589 7.319 6336 Z= 0.315 Chirality : 0.041 0.155 780 Planarity : 0.003 0.044 762 Dihedral : 4.015 17.905 624 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 6.32 % Allowed : 30.04 % Favored : 63.64 % 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: 2.43 (0.37), residues: 574 helix: 2.74 (0.25), residues: 384 sheet: -1.18 (0.76), residues: 52 loop : -0.58 (0.64), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.007 0.001 HIS A 395 PHE 0.013 0.001 PHE A 312 TYR 0.012 0.001 TYR A 404 ARG 0.005 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 329) hydrogen bonds : angle 3.61607 ( 987) covalent geometry : bond 0.00344 ( 4670) covalent geometry : angle 0.58874 ( 6336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.532 Fit side-chains REVERT: B 189 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8475 (tt) REVERT: B 204 GLN cc_start: 0.7721 (tp40) cc_final: 0.7374 (mp10) REVERT: B 210 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.7942 (p0) REVERT: B 285 SER cc_start: 0.8972 (m) cc_final: 0.8600 (t) REVERT: A 189 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8456 (tt) REVERT: A 285 SER cc_start: 0.8976 (m) cc_final: 0.8607 (t) REVERT: A 302 LYS cc_start: 0.9122 (tptm) cc_final: 0.8781 (tptp) REVERT: A 359 ASP cc_start: 0.8124 (t0) cc_final: 0.7585 (t0) REVERT: A 360 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8845 (tt) outliers start: 32 outliers final: 24 residues processed: 130 average time/residue: 0.1064 time to fit residues: 19.4264 Evaluate side-chains 139 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.097038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.076433 restraints weight = 9089.306| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.02 r_work: 0.2889 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4670 Z= 0.188 Angle : 0.610 7.365 6336 Z= 0.329 Chirality : 0.042 0.162 780 Planarity : 0.004 0.045 762 Dihedral : 4.077 19.615 624 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 5.93 % Allowed : 31.82 % Favored : 62.25 % 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: 2.53 (0.37), residues: 574 helix: 2.76 (0.25), residues: 380 sheet: -1.11 (0.76), residues: 52 loop : -0.27 (0.64), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 162 HIS 0.007 0.001 HIS A 395 PHE 0.013 0.001 PHE A 312 TYR 0.012 0.001 TYR B 404 ARG 0.005 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 329) hydrogen bonds : angle 3.70842 ( 987) covalent geometry : bond 0.00437 ( 4670) covalent geometry : angle 0.60999 ( 6336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.542 Fit side-chains REVERT: B 189 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8529 (tt) REVERT: B 204 GLN cc_start: 0.7735 (tp40) cc_final: 0.7381 (mp10) REVERT: B 210 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.7827 (p0) REVERT: B 285 SER cc_start: 0.8990 (m) cc_final: 0.8633 (t) REVERT: B 359 ASP cc_start: 0.8308 (t0) cc_final: 0.7730 (t0) REVERT: A 189 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8504 (tt) REVERT: A 285 SER cc_start: 0.8974 (m) cc_final: 0.8620 (t) REVERT: A 302 LYS cc_start: 0.9156 (tptm) cc_final: 0.8823 (tptp) REVERT: A 359 ASP cc_start: 0.8208 (t0) cc_final: 0.7645 (t0) REVERT: A 360 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8927 (tt) outliers start: 30 outliers final: 25 residues processed: 122 average time/residue: 0.1089 time to fit residues: 18.6821 Evaluate side-chains 130 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077632 restraints weight = 9081.713| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.04 r_work: 0.2949 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4670 Z= 0.156 Angle : 0.607 7.505 6336 Z= 0.325 Chirality : 0.041 0.162 780 Planarity : 0.004 0.044 762 Dihedral : 4.012 18.785 624 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.34 % Allowed : 32.02 % Favored : 62.65 % 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: 2.40 (0.37), residues: 574 helix: 2.68 (0.25), residues: 384 sheet: -1.06 (0.77), residues: 52 loop : -0.49 (0.65), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 162 HIS 0.007 0.001 HIS A 395 PHE 0.014 0.001 PHE A 312 TYR 0.012 0.001 TYR B 404 ARG 0.004 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 329) hydrogen bonds : angle 3.64980 ( 987) covalent geometry : bond 0.00358 ( 4670) covalent geometry : angle 0.60661 ( 6336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.621 Fit side-chains REVERT: B 189 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8491 (tt) REVERT: B 204 GLN cc_start: 0.7710 (tp40) cc_final: 0.7350 (mp10) REVERT: B 210 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7726 (p0) REVERT: B 285 SER cc_start: 0.8975 (m) cc_final: 0.8605 (t) REVERT: B 302 LYS cc_start: 0.9098 (tptm) cc_final: 0.8878 (tptm) REVERT: A 189 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8473 (tt) REVERT: A 285 SER cc_start: 0.8958 (m) cc_final: 0.8593 (t) REVERT: A 302 LYS cc_start: 0.9086 (tptm) cc_final: 0.8741 (tptp) REVERT: A 359 ASP cc_start: 0.8110 (t0) cc_final: 0.7531 (t0) outliers start: 27 outliers final: 22 residues processed: 124 average time/residue: 0.1412 time to fit residues: 24.4308 Evaluate side-chains 130 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.078561 restraints weight = 9278.544| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.02 r_work: 0.2939 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4670 Z= 0.143 Angle : 0.605 7.431 6336 Z= 0.323 Chirality : 0.041 0.160 780 Planarity : 0.004 0.044 762 Dihedral : 3.969 19.085 624 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.14 % Allowed : 32.21 % Favored : 62.65 % 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: 2.44 (0.37), residues: 574 helix: 2.71 (0.25), residues: 384 sheet: -1.03 (0.77), residues: 52 loop : -0.49 (0.65), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.006 0.001 HIS A 395 PHE 0.014 0.001 PHE B 312 TYR 0.012 0.001 TYR A 404 ARG 0.005 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 329) hydrogen bonds : angle 3.60065 ( 987) covalent geometry : bond 0.00324 ( 4670) covalent geometry : angle 0.60494 ( 6336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.825 Fit side-chains REVERT: B 189 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8455 (tt) REVERT: B 204 GLN cc_start: 0.7723 (tp40) cc_final: 0.7361 (mp10) REVERT: B 210 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7708 (p0) REVERT: B 285 SER cc_start: 0.8970 (m) cc_final: 0.8594 (t) REVERT: B 302 LYS cc_start: 0.9101 (tptm) cc_final: 0.8882 (tptm) REVERT: A 189 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8461 (tt) REVERT: A 285 SER cc_start: 0.8975 (m) cc_final: 0.8597 (t) REVERT: A 302 LYS cc_start: 0.9098 (tptm) cc_final: 0.8756 (tptp) REVERT: A 359 ASP cc_start: 0.8028 (t0) cc_final: 0.7474 (t0) REVERT: A 360 LEU cc_start: 0.9083 (tt) cc_final: 0.8755 (tt) outliers start: 26 outliers final: 22 residues processed: 133 average time/residue: 0.1447 time to fit residues: 27.3945 Evaluate side-chains 138 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 406 CYS Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.079454 restraints weight = 9123.552| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.06 r_work: 0.2977 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4670 Z= 0.144 Angle : 0.613 7.418 6336 Z= 0.328 Chirality : 0.041 0.158 780 Planarity : 0.004 0.044 762 Dihedral : 4.026 18.942 624 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.94 % Allowed : 33.60 % Favored : 61.46 % 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: 2.46 (0.37), residues: 574 helix: 2.71 (0.25), residues: 384 sheet: -0.99 (0.78), residues: 52 loop : -0.48 (0.65), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 162 HIS 0.006 0.001 HIS A 395 PHE 0.014 0.001 PHE A 312 TYR 0.011 0.001 TYR B 404 ARG 0.004 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 329) hydrogen bonds : angle 3.59267 ( 987) covalent geometry : bond 0.00328 ( 4670) covalent geometry : angle 0.61268 ( 6336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2431.11 seconds wall clock time: 43 minutes 1.87 seconds (2581.87 seconds total)