Starting phenix.real_space_refine on Wed Mar 5 22:40:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bim_44593/03_2025/9bim_44593.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bim_44593/03_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_44593/03_2025/9bim_44593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bim_44593/03_2025/9bim_44593.map" model { file = "/net/cci-nas-00/data/ceres_data/9bim_44593/03_2025/9bim_44593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bim_44593/03_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-5624/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: 2.73, per 1000 atoms: 0.68 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: 0.86 Conformation dependent library (CDL) restraints added in 418.4 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: 0.29 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: 1.18 Time building geometry restraints manager: 1.02 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: 1.040 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.540 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- 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 : 0.410 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: 0.2189 time to fit residues: 7.1134 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 : 0.418 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.143356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112940 restraints weight = 4121.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.115850 restraints weight = 2731.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.117861 restraints weight = 2072.694| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.0801 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 7.604 5614 Z= 0.284 Chirality : 0.039 0.138 647 Planarity : 0.004 0.025 680 Dihedral : 7.927 55.832 591 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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 : 0.405 Fit side-chains REVERT: A 106 MET cc_start: 0.7353 (mmt) cc_final: 0.6731 (mmt) REVERT: A 269 TYR cc_start: 0.8227 (m-10) cc_final: 0.7959 (m-80) REVERT: A 484 MET cc_start: 0.8595 (tmm) cc_final: 0.7804 (ttt) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.1936 time to fit residues: 6.1196 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 : 0.405 ------------------------------------------------------------------------------- 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: 0.7980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.139728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.108822 restraints weight = 4156.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111726 restraints weight = 2735.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.113462 restraints weight = 2111.569| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4106 Z= 0.225 Angle : 0.564 7.420 5614 Z= 0.280 Chirality : 0.040 0.139 647 Planarity : 0.004 0.024 680 Dihedral : 6.824 45.848 591 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.85 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: 1.02 (0.37), residues: 512 helix: 1.21 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -0.55 (0.49), residues: 147 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 0.009 0.001 PHE A 56 TYR 0.023 0.001 TYR A 67 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 27 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.401 Fit side-chains REVERT: A 106 MET cc_start: 0.7477 (mmt) cc_final: 0.6848 (mmt) REVERT: A 269 TYR cc_start: 0.8297 (m-10) cc_final: 0.7927 (m-80) outliers start: 5 outliers final: 2 residues processed: 24 average time/residue: 0.2261 time to fit residues: 7.1244 Evaluate side-chains 23 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL 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: 0.0970 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.141280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.110240 restraints weight = 4162.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.113228 restraints weight = 2729.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.115318 restraints weight = 2075.348| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1277 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= 0.185 Angle : 0.534 8.121 5614 Z= 0.265 Chirality : 0.039 0.143 647 Planarity : 0.004 0.027 680 Dihedral : 6.377 42.479 591 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.21 % Allowed : 9.66 % 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: 1.43 (0.38), residues: 512 helix: 1.49 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.43 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.006 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: 5 poor density : 24 time to evaluate : 0.378 Fit side-chains REVERT: A 109 LYS cc_start: 0.7394 (pttm) cc_final: 0.7126 (ptpt) REVERT: A 269 TYR cc_start: 0.8270 (m-10) cc_final: 0.7821 (m-80) REVERT: A 397 LEU cc_start: 0.8234 (mt) cc_final: 0.7952 (mt) REVERT: A 484 MET cc_start: 0.8641 (tmm) cc_final: 0.7835 (ttt) outliers start: 5 outliers final: 3 residues processed: 26 average time/residue: 0.1983 time to fit residues: 6.6100 Evaluate side-chains 27 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 399 THR 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: 0.9980 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.138070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.106921 restraints weight = 4317.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109893 restraints weight = 2826.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111895 restraints weight = 2164.107| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4106 Z= 0.226 Angle : 0.558 8.459 5614 Z= 0.275 Chirality : 0.039 0.142 647 Planarity : 0.004 0.025 680 Dihedral : 6.349 42.909 591 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.66 % Allowed : 8.45 % 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: 1.40 (0.38), residues: 512 helix: 1.47 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.42 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 24 HIS 0.002 0.000 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.022 0.001 TYR A 67 ARG 0.006 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: 11 poor density : 24 time to evaluate : 0.417 Fit side-chains REVERT: A 109 LYS cc_start: 0.7426 (pttm) cc_final: 0.7164 (ptpt) REVERT: A 187 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8113 (m) REVERT: A 380 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7888 (p) REVERT: A 484 MET cc_start: 0.8636 (tmm) cc_final: 0.7759 (ttt) outliers start: 11 outliers final: 4 residues processed: 32 average time/residue: 0.1848 time to fit residues: 7.7118 Evaluate side-chains 29 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 15 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.140921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.110262 restraints weight = 4121.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.113259 restraints weight = 2693.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.115330 restraints weight = 2052.732| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4106 Z= 0.161 Angle : 0.514 7.330 5614 Z= 0.254 Chirality : 0.038 0.139 647 Planarity : 0.003 0.026 680 Dihedral : 5.792 37.538 591 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.66 % Allowed : 8.70 % 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: 1.68 (0.38), residues: 512 helix: 1.68 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.34 (0.50), 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 0.007 0.001 PHE A 479 TYR 0.022 0.001 TYR A 175 ARG 0.006 0.000 ARG A 38 *********************** 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 37 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.440 Fit side-chains REVERT: A 139 MET cc_start: 0.7035 (mmm) cc_final: 0.5384 (mtp) REVERT: A 187 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.8044 (m) outliers start: 11 outliers final: 7 residues processed: 33 average time/residue: 0.1915 time to fit residues: 8.1407 Evaluate side-chains 33 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP 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 Chi-restraints excluded: chain A residue 422 LEU 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: 0.6980 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.0170 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.142964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111950 restraints weight = 4126.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115054 restraints weight = 2679.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116981 restraints weight = 2035.325| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1600 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= 0.149 Angle : 0.502 6.969 5614 Z= 0.249 Chirality : 0.038 0.138 647 Planarity : 0.003 0.027 680 Dihedral : 5.377 33.315 591 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.66 % Allowed : 8.94 % 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: 1.95 (0.38), residues: 512 helix: 1.87 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.12 (0.51), residues: 145 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 0.007 0.001 PHE A 479 TYR 0.023 0.001 TYR A 175 ARG 0.008 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 36 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.412 Fit side-chains REVERT: A 187 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7954 (m) REVERT: A 484 MET cc_start: 0.8645 (tmm) cc_final: 0.7933 (ttt) outliers start: 11 outliers final: 7 residues processed: 31 average time/residue: 0.1882 time to fit residues: 7.4802 Evaluate side-chains 33 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP 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 358 MET 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: 0.0370 chunk 18 optimal weight: 0.0030 chunk 47 optimal weight: 0.1980 chunk 41 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.2468 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.146039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115745 restraints weight = 4059.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118912 restraints weight = 2631.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120971 restraints weight = 1978.980| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4106 Z= 0.129 Angle : 0.499 7.960 5614 Z= 0.244 Chirality : 0.037 0.136 647 Planarity : 0.003 0.027 680 Dihedral : 4.890 27.890 591 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.93 % Allowed : 9.90 % 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: 2.12 (0.38), residues: 512 helix: 2.02 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -0.10 (0.50), residues: 146 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 0.008 0.001 PHE A 418 TYR 0.023 0.001 TYR A 175 ARG 0.007 0.001 ARG A 369 *********************** 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: 8 poor density : 24 time to evaluate : 0.402 Fit side-chains REVERT: A 139 MET cc_start: 0.7003 (mmm) cc_final: 0.5277 (mtp) REVERT: A 187 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7824 (m) REVERT: A 358 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7806 (mtp) REVERT: A 484 MET cc_start: 0.8598 (tmm) cc_final: 0.7856 (ttt) outliers start: 8 outliers final: 5 residues processed: 28 average time/residue: 0.2083 time to fit residues: 7.5706 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE 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 358 MET 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: 0.0060 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.141971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111327 restraints weight = 4123.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.114353 restraints weight = 2712.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116205 restraints weight = 2078.639| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4106 Z= 0.179 Angle : 0.521 7.318 5614 Z= 0.255 Chirality : 0.038 0.138 647 Planarity : 0.004 0.029 680 Dihedral : 5.179 31.992 591 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.17 % Allowed : 9.90 % Favored : 87.92 % 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: 1.86 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.25 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 141 HIS 0.002 0.000 HIS A 162 PHE 0.007 0.001 PHE A 244 TYR 0.021 0.001 TYR A 175 ARG 0.007 0.001 ARG A 369 *********************** 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 33 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.418 Fit side-chains REVERT: A 139 MET cc_start: 0.7067 (mmm) cc_final: 0.5380 (mtp) REVERT: A 484 MET cc_start: 0.8625 (tmm) cc_final: 0.7899 (ttt) outliers start: 9 outliers final: 7 residues processed: 28 average time/residue: 0.2064 time to fit residues: 7.4745 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 : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP 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 358 MET 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: 0.0470 chunk 23 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.138265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.107383 restraints weight = 4164.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.110212 restraints weight = 2800.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111923 restraints weight = 2182.299| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4106 Z= 0.229 Angle : 0.560 8.289 5614 Z= 0.275 Chirality : 0.040 0.142 647 Planarity : 0.004 0.030 680 Dihedral : 5.713 37.763 591 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.93 % Allowed : 10.14 % Favored : 87.92 % 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: 1.72 (0.38), residues: 512 helix: 1.67 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.20 (0.52), 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 0.010 0.001 PHE A 56 TYR 0.023 0.001 TYR A 67 ARG 0.007 0.001 ARG A 369 ********************** 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 32 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.359 Fit side-chains REVERT: A 106 MET cc_start: 0.7502 (tpp) cc_final: 0.7012 (mmt) REVERT: A 484 MET cc_start: 0.8637 (tmm) cc_final: 0.7909 (ttt) outliers start: 8 outliers final: 7 residues processed: 28 average time/residue: 0.1953 time to fit residues: 6.9871 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 : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 177 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: 0.0570 chunk 41 optimal weight: 0.0170 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.141801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111340 restraints weight = 4078.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.114435 restraints weight = 2654.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116462 restraints weight = 2013.532| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1799 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= 0.159 Angle : 0.524 8.548 5614 Z= 0.256 Chirality : 0.038 0.138 647 Planarity : 0.004 0.030 680 Dihedral : 5.303 33.279 591 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.45 % Allowed : 10.63 % Favored : 87.92 % 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: 1.86 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -0.17 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 240 HIS 0.001 0.000 HIS A 162 PHE 0.012 0.001 PHE A 56 TYR 0.022 0.001 TYR A 175 ARG 0.007 0.001 ARG A 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1440.79 seconds wall clock time: 25 minutes 44.29 seconds (1544.29 seconds total)