Starting phenix.real_space_refine on Mon Jan 13 20:21:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bim_44593/01_2025/9bim_44593.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bim_44593/01_2025/9bim_44593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bim_44593/01_2025/9bim_44593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bim_44593/01_2025/9bim_44593.map" model { file = "/net/cci-nas-00/data/ceres_data/9bim_44593/01_2025/9bim_44593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bim_44593/01_2025/9bim_44593.cif" } resolution = 3.67 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= 0.207 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 20 5.16 5 C 2665 2.51 5 N 605 2.21 5 O 702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3992 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3962 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 493} Chain breaks: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'HC6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.14, per 1000 atoms: 0.79 Number of scatterers: 3992 At special positions: 0 Unit cell: (58.8, 83.16, 84, 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 20 16.00 O 702 8.00 N 605 7.00 C 2665 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: 1.24 Conformation dependent library (CDL) restraints added in 792.5 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 73.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 3.737A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.092A pdb=" N ILE A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 44' Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 86 through 102 Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.611A pdb=" N MET A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 157 removed outlier: 3.501A pdb=" N ILE A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ARG A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 160 through 179 removed outlier: 3.671A pdb=" N SER A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 208 removed outlier: 3.969A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.714A pdb=" N ALA A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 254 through 263 removed outlier: 4.321A pdb=" N ARG A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 298 removed outlier: 3.529A pdb=" N GLN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 319 through 327 Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.604A pdb=" N PHE A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 399 Processing helix chain 'A' and resid 401 through 426 removed outlier: 3.631A pdb=" N LEU A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.757A pdb=" N LEU A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 450 removed outlier: 3.544A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 262 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 1.21 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: 1153 1.34 - 1.46: 753 1.46 - 1.57: 2165 1.57 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 4106 Sorted by residual: bond pdb=" CAS HC6 A 701 " pdb=" OBD HC6 A 701 " ideal model delta sigma weight residual 1.389 1.430 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" CAB HC6 A 701 " pdb=" NAA HC6 A 701 " ideal model delta sigma weight residual 1.500 1.459 0.041 2.00e-02 2.50e+03 4.16e+00 bond pdb=" CAC HC6 A 701 " pdb=" NAA HC6 A 701 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.00e-02 2.50e+03 3.06e+00 bond pdb=" CAD HC6 A 701 " pdb=" OBC HC6 A 701 " ideal model delta sigma weight residual 1.389 1.423 -0.034 2.00e-02 2.50e+03 2.98e+00 bond pdb=" CAX HC6 A 701 " pdb=" NAW HC6 A 701 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.00e-02 2.50e+03 2.81e+00 ... (remaining 4101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 5478 2.04 - 4.07: 104 4.07 - 6.11: 22 6.11 - 8.14: 9 8.14 - 10.18: 1 Bond angle restraints: 5614 Sorted by residual: angle pdb=" CA TYR A 175 " pdb=" CB TYR A 175 " pdb=" CG TYR A 175 " ideal model delta sigma weight residual 113.90 119.67 -5.77 1.80e+00 3.09e-01 1.03e+01 angle pdb=" N GLY A 179 " pdb=" CA GLY A 179 " pdb=" C GLY A 179 " ideal model delta sigma weight residual 113.18 120.19 -7.01 2.37e+00 1.78e-01 8.75e+00 angle pdb=" CA LEU A 273 " pdb=" CB LEU A 273 " pdb=" CG LEU A 273 " ideal model delta sigma weight residual 116.30 126.48 -10.18 3.50e+00 8.16e-02 8.46e+00 angle pdb=" C VAL A 178 " pdb=" N GLY A 179 " pdb=" CA GLY A 179 " ideal model delta sigma weight residual 121.41 115.93 5.48 1.96e+00 2.60e-01 7.81e+00 angle pdb=" CG ARG A 38 " pdb=" CD ARG A 38 " pdb=" NE ARG A 38 " ideal model delta sigma weight residual 112.00 118.13 -6.13 2.20e+00 2.07e-01 7.76e+00 ... (remaining 5609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.67: 2101 14.67 - 29.33: 179 29.33 - 44.00: 61 44.00 - 58.66: 4 58.66 - 73.33: 7 Dihedral angle restraints: 2352 sinusoidal: 869 harmonic: 1483 Sorted by residual: dihedral pdb=" CA LYS A 109 " pdb=" C LYS A 109 " pdb=" N GLY A 110 " pdb=" CA GLY A 110 " ideal model delta harmonic sigma weight residual -180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA MET A 114 " pdb=" C MET A 114 " pdb=" N LEU A 115 " pdb=" CA LEU A 115 " ideal model delta harmonic sigma weight residual 180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLY A 7 " pdb=" C GLY A 7 " pdb=" N LEU A 8 " pdb=" CA LEU A 8 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 2349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 476 0.045 - 0.090: 132 0.090 - 0.136: 33 0.136 - 0.181: 5 0.181 - 0.226: 1 Chirality restraints: 647 Sorted by residual: chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL A 184 " pdb=" CA VAL A 184 " pdb=" CG1 VAL A 184 " pdb=" CG2 VAL A 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CB ILE A 157 " pdb=" CA ILE A 157 " pdb=" CG1 ILE A 157 " pdb=" CG2 ILE A 157 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 644 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 175 " 0.012 2.00e-02 2.50e+03 1.05e-02 2.19e+00 pdb=" CG TYR A 175 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 175 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 175 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 175 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 175 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 175 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 175 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 418 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.02e+00 pdb=" N PRO A 419 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 116 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 117 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.018 5.00e-02 4.00e+02 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 944 2.79 - 3.32: 3830 3.32 - 3.84: 6747 3.84 - 4.37: 7356 4.37 - 4.90: 13195 Nonbonded interactions: 32072 Sorted by model distance: nonbonded pdb=" O ILE A 294 " pdb=" OG1 THR A 298 " model vdw 2.259 3.040 nonbonded pdb=" O VAL A 380 " pdb=" OG1 THR A 384 " model vdw 2.320 3.040 nonbonded pdb=" OD2 ASP A 309 " pdb=" NZ LYS A 311 " model vdw 2.361 3.120 nonbonded pdb=" O ALA A 60 " pdb=" OG SER A 346 " model vdw 2.450 3.040 nonbonded pdb=" OH TYR A 305 " pdb=" OE1 GLU A 315 " model vdw 2.458 3.040 ... (remaining 32067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.120 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 0.044 4106 Z= 0.249 Angle : 0.745 10.179 5614 Z= 0.365 Chirality : 0.045 0.226 647 Planarity : 0.005 0.040 680 Dihedral : 13.024 73.329 1414 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.00 (0.35), residues: 512 helix: 0.49 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -0.97 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 62 HIS 0.002 0.001 HIS A 162 PHE 0.021 0.002 PHE A 258 TYR 0.026 0.002 TYR A 175 ARG 0.010 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.356 Fit side-chains REVERT: A 106 MET cc_start: 0.7221 (mmt) cc_final: 0.6655 (mmt) REVERT: A 269 TYR cc_start: 0.8135 (m-10) cc_final: 0.7855 (m-10) REVERT: A 484 MET cc_start: 0.8321 (tmm) cc_final: 0.7986 (ttt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1920 time to fit residues: 6.2080 Evaluate side-chains 22 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.0470 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 0.0050 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 overall best weight: 0.7296 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.143326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112839 restraints weight = 4123.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.115772 restraints weight = 2703.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117863 restraints weight = 2061.060| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4106 Z= 0.209 Angle : 0.571 7.613 5614 Z= 0.285 Chirality : 0.040 0.138 647 Planarity : 0.004 0.026 680 Dihedral : 7.892 55.516 591 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.48 % Allowed : 6.04 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.84 (0.37), residues: 512 helix: 1.10 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.69 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.002 0.000 HIS A 162 PHE 0.010 0.001 PHE A 244 TYR 0.022 0.001 TYR A 67 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.364 Fit side-chains REVERT: A 106 MET cc_start: 0.7349 (mmt) cc_final: 0.6724 (mmt) REVERT: A 269 TYR cc_start: 0.8228 (m-10) cc_final: 0.7958 (m-80) REVERT: A 484 MET cc_start: 0.8595 (tmm) cc_final: 0.7801 (ttt) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.1914 time to fit residues: 6.0317 Evaluate side-chains 22 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 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 = 0.3531 r_free = 0.3531 target = 0.140975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110291 restraints weight = 4136.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113043 restraints weight = 2725.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.115169 restraints weight = 2090.290| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4106 Z= 0.203 Angle : 0.550 7.012 5614 Z= 0.273 Chirality : 0.039 0.138 647 Planarity : 0.003 0.024 680 Dihedral : 6.507 42.713 591 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.21 % Allowed : 8.94 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.25 (0.37), residues: 512 helix: 1.32 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.36 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.002 0.000 HIS A 162 PHE 0.008 0.001 PHE A 56 TYR 0.022 0.001 TYR A 175 ARG 0.003 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.425 Fit side-chains REVERT: A 106 MET cc_start: 0.7416 (mmt) cc_final: 0.6830 (mmt) REVERT: A 109 LYS cc_start: 0.7341 (pttm) cc_final: 0.7043 (ptpt) REVERT: A 269 TYR cc_start: 0.8279 (m-10) cc_final: 0.7904 (m-80) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.2143 time to fit residues: 6.8239 Evaluate side-chains 25 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 46 optimal weight: 0.0670 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.0570 chunk 21 optimal weight: 0.5980 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.144188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.113398 restraints weight = 4134.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116561 restraints weight = 2643.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.118740 restraints weight = 1986.849| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4106 Z= 0.148 Angle : 0.512 7.364 5614 Z= 0.253 Chirality : 0.038 0.141 647 Planarity : 0.003 0.024 680 Dihedral : 5.954 38.213 591 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.72 % Allowed : 9.66 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.63 (0.38), residues: 512 helix: 1.65 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.39 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 240 HIS 0.001 0.000 HIS A 162 PHE 0.007 0.001 PHE A 56 TYR 0.023 0.001 TYR A 175 ARG 0.006 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.467 Fit side-chains REVERT: A 109 LYS cc_start: 0.7338 (pttm) cc_final: 0.7088 (ptpt) REVERT: A 269 TYR cc_start: 0.8221 (m-10) cc_final: 0.7811 (m-80) REVERT: A 358 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8048 (mtp) REVERT: A 397 LEU cc_start: 0.8215 (mt) cc_final: 0.7945 (mt) REVERT: A 484 MET cc_start: 0.8654 (tmm) cc_final: 0.7825 (ttt) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.2043 time to fit residues: 7.1426 Evaluate side-chains 27 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.0270 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 overall best weight: 0.5916 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.141608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110650 restraints weight = 4261.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.113733 restraints weight = 2746.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.115907 restraints weight = 2072.524| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4106 Z= 0.177 Angle : 0.531 7.803 5614 Z= 0.259 Chirality : 0.038 0.140 647 Planarity : 0.003 0.026 680 Dihedral : 5.773 37.191 591 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.42 % Allowed : 8.45 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.68 (0.38), residues: 512 helix: 1.68 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -0.38 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 240 HIS 0.002 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.021 0.001 TYR A 175 ARG 0.007 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.427 Fit side-chains REVERT: A 109 LYS cc_start: 0.7391 (pttm) cc_final: 0.7138 (ptpt) REVERT: A 139 MET cc_start: 0.6972 (mmm) cc_final: 0.5400 (mtp) REVERT: A 187 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.8031 (m) REVERT: A 380 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7865 (p) REVERT: A 484 MET cc_start: 0.8623 (tmm) cc_final: 0.7772 (ttt) outliers start: 10 outliers final: 3 residues processed: 32 average time/residue: 0.1859 time to fit residues: 7.7105 Evaluate side-chains 29 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.140090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109921 restraints weight = 4107.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112765 restraints weight = 2738.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114690 restraints weight = 2116.050| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4106 Z= 0.182 Angle : 0.517 7.696 5614 Z= 0.257 Chirality : 0.038 0.140 647 Planarity : 0.004 0.027 680 Dihedral : 5.679 36.614 591 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.17 % Allowed : 8.94 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.69 (0.38), residues: 512 helix: 1.69 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.35 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 141 HIS 0.002 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.022 0.001 TYR A 175 ARG 0.006 0.001 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.376 Fit side-chains REVERT: A 187 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.8024 (m) REVERT: A 484 MET cc_start: 0.8644 (tmm) cc_final: 0.7761 (ttt) outliers start: 9 outliers final: 5 residues processed: 31 average time/residue: 0.1929 time to fit residues: 7.7063 Evaluate side-chains 30 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 45 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.139971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109131 restraints weight = 4162.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.112065 restraints weight = 2758.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114069 restraints weight = 2118.849| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4106 Z= 0.192 Angle : 0.529 7.670 5614 Z= 0.261 Chirality : 0.039 0.140 647 Planarity : 0.004 0.028 680 Dihedral : 5.641 36.416 591 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.42 % Allowed : 8.45 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.71 (0.38), residues: 512 helix: 1.72 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.38 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 240 HIS 0.002 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.022 0.001 TYR A 175 ARG 0.007 0.001 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.405 Fit side-chains REVERT: A 139 MET cc_start: 0.7026 (mmm) cc_final: 0.5413 (ttp) REVERT: A 187 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7996 (m) REVERT: A 484 MET cc_start: 0.8663 (tmm) cc_final: 0.7783 (ttt) outliers start: 10 outliers final: 5 residues processed: 31 average time/residue: 0.1995 time to fit residues: 7.9576 Evaluate side-chains 31 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 46 optimal weight: 0.0070 chunk 18 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 28 optimal weight: 0.0370 chunk 4 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.143499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112822 restraints weight = 4089.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115889 restraints weight = 2677.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118148 restraints weight = 2021.799| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4106 Z= 0.147 Angle : 0.504 6.733 5614 Z= 0.247 Chirality : 0.037 0.137 647 Planarity : 0.003 0.028 680 Dihedral : 5.130 30.698 591 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.69 % Allowed : 9.90 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.05 (0.38), residues: 512 helix: 1.93 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -0.09 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 240 HIS 0.001 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.022 0.001 TYR A 175 ARG 0.007 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.421 Fit side-chains REVERT: A 187 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7910 (m) REVERT: A 484 MET cc_start: 0.8639 (tmm) cc_final: 0.7755 (ttt) outliers start: 7 outliers final: 4 residues processed: 29 average time/residue: 0.2039 time to fit residues: 7.6204 Evaluate side-chains 29 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 19 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.139350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108613 restraints weight = 4154.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111489 restraints weight = 2785.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.113142 restraints weight = 2159.213| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4106 Z= 0.208 Angle : 0.546 8.097 5614 Z= 0.266 Chirality : 0.039 0.140 647 Planarity : 0.004 0.028 680 Dihedral : 5.500 35.435 591 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.69 % Allowed : 9.66 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.78 (0.38), residues: 512 helix: 1.72 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.20 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 406 HIS 0.002 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.021 0.001 TYR A 175 ARG 0.006 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.366 Fit side-chains REVERT: A 106 MET cc_start: 0.7505 (tpp) cc_final: 0.7053 (mmt) REVERT: A 139 MET cc_start: 0.6983 (mmm) cc_final: 0.5503 (ttp) REVERT: A 484 MET cc_start: 0.8670 (tmm) cc_final: 0.7781 (ttt) outliers start: 7 outliers final: 5 residues processed: 28 average time/residue: 0.1857 time to fit residues: 6.6369 Evaluate side-chains 29 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 45 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 23 optimal weight: 0.0040 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.141563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.110707 restraints weight = 4123.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113785 restraints weight = 2725.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115509 restraints weight = 2075.720| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4106 Z= 0.168 Angle : 0.526 7.707 5614 Z= 0.257 Chirality : 0.038 0.139 647 Planarity : 0.003 0.030 680 Dihedral : 5.314 33.197 591 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.21 % Allowed : 10.63 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.93 (0.38), residues: 512 helix: 1.84 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.14 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 240 HIS 0.002 0.000 HIS A 162 PHE 0.008 0.001 PHE A 56 TYR 0.022 0.001 TYR A 175 ARG 0.007 0.001 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.379 Fit side-chains REVERT: A 106 MET cc_start: 0.7462 (tpp) cc_final: 0.6981 (mmt) REVERT: A 139 MET cc_start: 0.7071 (mmm) cc_final: 0.5443 (ttp) REVERT: A 484 MET cc_start: 0.8650 (tmm) cc_final: 0.7756 (ttt) outliers start: 5 outliers final: 5 residues processed: 26 average time/residue: 0.2184 time to fit residues: 7.3227 Evaluate side-chains 28 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.139056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.108831 restraints weight = 4114.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111670 restraints weight = 2745.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.113615 restraints weight = 2117.021| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4106 Z= 0.213 Angle : 0.548 8.210 5614 Z= 0.268 Chirality : 0.039 0.140 647 Planarity : 0.004 0.029 680 Dihedral : 5.559 36.080 591 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.45 % Allowed : 10.14 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.78 (0.38), residues: 512 helix: 1.72 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.21 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 406 HIS 0.002 0.000 HIS A 162 PHE 0.011 0.001 PHE A 56 TYR 0.022 0.001 TYR A 175 ARG 0.007 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.28 seconds wall clock time: 25 minutes 57.12 seconds (1557.12 seconds total)