Starting phenix.real_space_refine on Wed Mar 5 21:49:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfj_44498/03_2025/9bfj_44498.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfj_44498/03_2025/9bfj_44498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bfj_44498/03_2025/9bfj_44498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfj_44498/03_2025/9bfj_44498.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfj_44498/03_2025/9bfj_44498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfj_44498/03_2025/9bfj_44498.cif" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.100 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: 6 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2564 2.51 5 N 578 2.21 5 O 669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3833 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3824 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Chain breaks: 2 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Unusual residues: {' CL': 1, ' NA': 1, 'CHT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.22, per 1000 atoms: 0.84 Number of scatterers: 3833 At special positions: 0 Unit cell: (73.062, 82.656, 74.538, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 20 16.00 Na 1 11.00 O 669 8.00 N 578 7.00 C 2564 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: 1.04 Conformation dependent library (CDL) restraints added in 483.5 milliseconds 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 78.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 3.805A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 63 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 81 through 84 Processing helix chain 'A' and resid 85 through 102 removed outlier: 4.701A pdb=" N ILE A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 95 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 123 through 157 removed outlier: 3.701A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 160 through 182 removed outlier: 3.582A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 208 Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 221 removed outlier: 4.043A 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: 4.027A pdb=" N ARG A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 297 Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 329 through 363 removed outlier: 4.010A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 399 Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.981A pdb=" N LEU A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 426 removed outlier: 4.327A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 449 Processing helix chain 'A' and resid 478 through 505 Processing helix chain 'A' and resid 508 through 512 Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 277 hydrogen bonds defined for protein. 819 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: 1.24 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1110 1.34 - 1.46: 920 1.46 - 1.58: 1875 1.58 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 3940 Sorted by residual: bond pdb=" C5 CHT A 801 " pdb=" N1 CHT A 801 " ideal model delta sigma weight residual 1.509 1.455 0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C8 CHT A 801 " pdb=" N1 CHT A 801 " ideal model delta sigma weight residual 1.492 1.440 0.052 2.00e-02 2.50e+03 6.82e+00 bond pdb=" C7 CHT A 801 " pdb=" N1 CHT A 801 " ideal model delta sigma weight residual 1.492 1.458 0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C6 CHT A 801 " pdb=" N1 CHT A 801 " ideal model delta sigma weight residual 1.487 1.460 0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" C ILE A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.37e+00 ... (remaining 3935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 5258 1.77 - 3.54: 100 3.54 - 5.30: 12 5.30 - 7.07: 10 7.07 - 8.84: 2 Bond angle restraints: 5382 Sorted by residual: angle pdb=" CA LEU A 273 " pdb=" CB LEU A 273 " pdb=" CG LEU A 273 " ideal model delta sigma weight residual 116.30 125.14 -8.84 3.50e+00 8.16e-02 6.38e+00 angle pdb=" CA ILE A 383 " pdb=" CB ILE A 383 " pdb=" CG1 ILE A 383 " ideal model delta sigma weight residual 110.40 114.60 -4.20 1.70e+00 3.46e-01 6.11e+00 angle pdb=" OG1 THR A 313 " pdb=" CB THR A 313 " pdb=" CG2 THR A 313 " ideal model delta sigma weight residual 109.30 104.91 4.39 2.00e+00 2.50e-01 4.82e+00 angle pdb=" C ASP A 309 " pdb=" CA ASP A 309 " pdb=" CB ASP A 309 " ideal model delta sigma weight residual 109.51 113.53 -4.02 1.85e+00 2.92e-01 4.73e+00 angle pdb=" C ILE A 252 " pdb=" N PRO A 253 " pdb=" CD PRO A 253 " ideal model delta sigma weight residual 125.00 133.23 -8.23 4.10e+00 5.95e-02 4.03e+00 ... (remaining 5377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 1985 17.11 - 34.21: 190 34.21 - 51.32: 42 51.32 - 68.42: 9 68.42 - 85.53: 6 Dihedral angle restraints: 2232 sinusoidal: 804 harmonic: 1428 Sorted by residual: dihedral pdb=" CG LYS A 226 " pdb=" CD LYS A 226 " pdb=" CE LYS A 226 " pdb=" NZ LYS A 226 " ideal model delta sinusoidal sigma weight residual -60.00 -117.13 57.13 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N LEU A 51 " pdb=" CA LEU A 51 " pdb=" CB LEU A 51 " pdb=" CG LEU A 51 " ideal model delta sinusoidal sigma weight residual -60.00 -114.52 54.52 3 1.50e+01 4.44e-03 9.29e+00 dihedral pdb=" CA MET A 395 " pdb=" CB MET A 395 " pdb=" CG MET A 395 " pdb=" SD MET A 395 " ideal model delta sinusoidal sigma weight residual 180.00 126.17 53.83 3 1.50e+01 4.44e-03 9.24e+00 ... (remaining 2229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 330 0.028 - 0.057: 189 0.057 - 0.085: 69 0.085 - 0.113: 23 0.113 - 0.141: 13 Chirality restraints: 624 Sorted by residual: chirality pdb=" CB VAL A 424 " pdb=" CA VAL A 424 " pdb=" CG1 VAL A 424 " pdb=" CG2 VAL A 424 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CB VAL A 380 " pdb=" CA VAL A 380 " pdb=" CG1 VAL A 380 " pdb=" CG2 VAL A 380 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA PRO A 310 " pdb=" N PRO A 310 " pdb=" C PRO A 310 " pdb=" CB PRO A 310 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 621 not shown) Planarity restraints: 651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 242 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C ASP A 242 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP A 242 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 243 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 67 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.69e+00 pdb=" C TYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR A 67 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 68 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 240 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C TRP A 240 " 0.031 2.00e-02 2.50e+03 pdb=" O TRP A 240 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 241 " -0.010 2.00e-02 2.50e+03 ... (remaining 648 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 238 2.74 - 3.28: 3920 3.28 - 3.82: 6814 3.82 - 4.36: 7880 4.36 - 4.90: 13608 Nonbonded interactions: 32460 Sorted by model distance: nonbonded pdb=" O VAL A 63 " pdb="NA NA A 803 " model vdw 2.196 2.470 nonbonded pdb=" O GLY A 389 " pdb=" OG1 THR A 393 " model vdw 2.218 3.040 nonbonded pdb=" O ALA A 60 " pdb="NA NA A 803 " model vdw 2.226 2.470 nonbonded pdb=" O ALA A 169 " pdb=" OG1 THR A 173 " model vdw 2.248 3.040 nonbonded pdb=" O ASN A 491 " pdb=" OG SER A 495 " model vdw 2.262 3.040 ... (remaining 32455 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.810 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:16.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 : 0.005 0.054 3940 Z= 0.307 Angle : 0.654 8.840 5382 Z= 0.342 Chirality : 0.043 0.141 624 Planarity : 0.006 0.037 651 Dihedral : 15.095 85.531 1328 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % 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: 0.78 (0.36), residues: 490 helix: 0.87 (0.25), residues: 374 sheet: None (None), residues: 0 loop : -0.38 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 379 HIS 0.002 0.001 HIS A 209 PHE 0.013 0.002 PHE A 3 TYR 0.020 0.002 TYR A 269 ARG 0.008 0.001 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.365 Fit side-chains REVERT: A 382 ARG cc_start: 0.7089 (mtt180) cc_final: 0.6784 (mtm-85) REVERT: A 386 PHE cc_start: 0.7753 (m-80) cc_final: 0.6674 (t80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.9541 time to fit residues: 48.8688 Evaluate side-chains 46 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.0170 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.0770 overall best weight: 0.5376 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.152005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105343 restraints weight = 4016.763| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.10 r_work: 0.3045 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3940 Z= 0.145 Angle : 0.475 6.580 5382 Z= 0.247 Chirality : 0.036 0.123 624 Planarity : 0.004 0.032 651 Dihedral : 4.515 57.972 535 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.75 % Allowed : 11.72 % Favored : 86.53 % 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: 1.89 (0.38), residues: 490 helix: 1.69 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.12 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 PHE 0.008 0.001 PHE A 244 TYR 0.012 0.001 TYR A 269 ARG 0.002 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.437 Fit side-chains REVERT: A 386 PHE cc_start: 0.7789 (m-80) cc_final: 0.6554 (t80) REVERT: A 400 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7960 (tptp) REVERT: A 428 LYS cc_start: 0.8122 (tmtm) cc_final: 0.7166 (tmmt) outliers start: 7 outliers final: 0 residues processed: 52 average time/residue: 0.8918 time to fit residues: 48.7062 Evaluate side-chains 51 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.151271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104665 restraints weight = 4080.355| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.26 r_work: 0.3065 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3940 Z= 0.175 Angle : 0.499 11.662 5382 Z= 0.251 Chirality : 0.037 0.126 624 Planarity : 0.004 0.030 651 Dihedral : 4.500 56.926 535 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.50 % Allowed : 11.72 % Favored : 86.78 % 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: 1.88 (0.38), residues: 490 helix: 1.72 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.29 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.007 0.001 PHE A 244 TYR 0.010 0.001 TYR A 269 ARG 0.001 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.392 Fit side-chains REVERT: A 386 PHE cc_start: 0.7861 (m-80) cc_final: 0.6627 (t80) REVERT: A 400 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7979 (tptp) outliers start: 6 outliers final: 0 residues processed: 53 average time/residue: 0.8382 time to fit residues: 46.7551 Evaluate side-chains 49 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.151874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104641 restraints weight = 4076.759| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.16 r_work: 0.3073 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3940 Z= 0.164 Angle : 0.479 8.209 5382 Z= 0.243 Chirality : 0.037 0.127 624 Planarity : 0.004 0.029 651 Dihedral : 4.301 50.584 535 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.00 % Allowed : 12.72 % Favored : 85.29 % 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: 1.96 (0.38), residues: 490 helix: 1.77 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.23 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 PHE 0.007 0.001 PHE A 196 TYR 0.009 0.001 TYR A 269 ARG 0.001 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.409 Fit side-chains REVERT: A 386 PHE cc_start: 0.7878 (m-80) cc_final: 0.6676 (t80) REVERT: A 400 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7972 (tptp) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 0.8557 time to fit residues: 47.6876 Evaluate side-chains 52 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.151230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104486 restraints weight = 4143.671| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.25 r_work: 0.3059 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3940 Z= 0.182 Angle : 0.485 6.843 5382 Z= 0.247 Chirality : 0.038 0.129 624 Planarity : 0.004 0.028 651 Dihedral : 4.192 44.101 535 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.50 % Allowed : 13.72 % Favored : 84.79 % 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: 1.81 (0.38), residues: 490 helix: 1.65 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.37 (0.58), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 PHE 0.008 0.001 PHE A 258 TYR 0.010 0.001 TYR A 331 ARG 0.001 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.421 Fit side-chains REVERT: A 386 PHE cc_start: 0.7858 (m-80) cc_final: 0.6595 (t80) REVERT: A 400 LYS cc_start: 0.8556 (mmtm) cc_final: 0.7915 (tptp) outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 0.8452 time to fit residues: 47.0363 Evaluate side-chains 49 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 178 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 8 optimal weight: 3.9990 chunk 48 optimal weight: 0.0010 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.151477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104229 restraints weight = 4101.872| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.17 r_work: 0.3066 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3940 Z= 0.177 Angle : 0.475 6.132 5382 Z= 0.243 Chirality : 0.037 0.127 624 Planarity : 0.004 0.027 651 Dihedral : 4.165 43.803 535 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.00 % Allowed : 13.97 % Favored : 84.04 % 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: 1.84 (0.38), residues: 490 helix: 1.68 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.35 (0.58), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 PHE 0.007 0.001 PHE A 258 TYR 0.009 0.001 TYR A 331 ARG 0.001 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.386 Fit side-chains REVERT: A 386 PHE cc_start: 0.7899 (m-80) cc_final: 0.6646 (t80) REVERT: A 400 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7933 (tptp) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.7627 time to fit residues: 41.8484 Evaluate side-chains 51 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.149778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104712 restraints weight = 4048.589| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.94 r_work: 0.3036 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3940 Z= 0.236 Angle : 0.515 6.418 5382 Z= 0.265 Chirality : 0.039 0.130 624 Planarity : 0.004 0.027 651 Dihedral : 4.269 42.005 535 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.00 % Allowed : 13.47 % Favored : 84.54 % 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: 490 helix: 1.57 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.37 (0.58), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.010 0.001 PHE A 258 TYR 0.011 0.001 TYR A 331 ARG 0.001 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.402 Fit side-chains REVERT: A 386 PHE cc_start: 0.7898 (m-80) cc_final: 0.6599 (t80) REVERT: A 400 LYS cc_start: 0.8580 (mmtm) cc_final: 0.7974 (tptp) outliers start: 8 outliers final: 4 residues processed: 56 average time/residue: 0.8051 time to fit residues: 47.4282 Evaluate side-chains 53 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 265 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105107 restraints weight = 4074.464| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.02 r_work: 0.3072 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 3940 Z= 0.164 Angle : 0.497 10.112 5382 Z= 0.250 Chirality : 0.037 0.124 624 Planarity : 0.004 0.027 651 Dihedral : 4.187 43.675 535 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.50 % Allowed : 13.97 % Favored : 84.54 % 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: 1.84 (0.38), residues: 490 helix: 1.67 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.32 (0.58), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 PHE 0.007 0.001 PHE A 258 TYR 0.008 0.001 TYR A 331 ARG 0.001 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.384 Fit side-chains REVERT: A 386 PHE cc_start: 0.7871 (m-80) cc_final: 0.6587 (t80) REVERT: A 400 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7953 (tptp) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.8556 time to fit residues: 47.7475 Evaluate side-chains 52 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.151525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104379 restraints weight = 4071.007| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.15 r_work: 0.3067 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3940 Z= 0.175 Angle : 0.500 9.618 5382 Z= 0.252 Chirality : 0.037 0.126 624 Planarity : 0.004 0.027 651 Dihedral : 4.175 43.384 535 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.50 % Allowed : 14.21 % Favored : 84.29 % 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: 1.86 (0.38), residues: 490 helix: 1.68 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.30 (0.58), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 PHE 0.007 0.001 PHE A 258 TYR 0.009 0.001 TYR A 331 ARG 0.000 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.437 Fit side-chains REVERT: A 386 PHE cc_start: 0.7905 (m-80) cc_final: 0.6642 (t80) REVERT: A 400 LYS cc_start: 0.8554 (mmtm) cc_final: 0.7899 (tptp) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.8118 time to fit residues: 43.6262 Evaluate side-chains 51 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 265 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.151968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104774 restraints weight = 4127.190| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.15 r_work: 0.3072 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3940 Z= 0.168 Angle : 0.494 9.557 5382 Z= 0.249 Chirality : 0.037 0.125 624 Planarity : 0.004 0.027 651 Dihedral : 4.154 43.546 535 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.50 % Allowed : 14.21 % Favored : 84.29 % 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: 1.90 (0.38), residues: 490 helix: 1.70 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.29 (0.58), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 PHE 0.007 0.001 PHE A 258 TYR 0.009 0.001 TYR A 331 ARG 0.001 0.000 ARG A 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.409 Fit side-chains REVERT: A 170 LEU cc_start: 0.7785 (tp) cc_final: 0.7439 (tt) REVERT: A 386 PHE cc_start: 0.7907 (m-80) cc_final: 0.6638 (t80) REVERT: A 400 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7877 (tptp) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.7622 time to fit residues: 41.8242 Evaluate side-chains 53 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 400 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 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 = 0.3815 r_free = 0.3815 target = 0.151937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104928 restraints weight = 4107.124| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.16 r_work: 0.3075 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3940 Z= 0.164 Angle : 0.491 9.358 5382 Z= 0.247 Chirality : 0.037 0.124 624 Planarity : 0.004 0.027 651 Dihedral : 4.138 43.593 535 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.50 % Allowed : 14.21 % Favored : 84.29 % 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: 1.94 (0.38), residues: 490 helix: 1.73 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.24 (0.59), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 PHE 0.007 0.001 PHE A 258 TYR 0.009 0.001 TYR A 331 ARG 0.000 0.000 ARG A 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3561.67 seconds wall clock time: 61 minutes 25.00 seconds (3685.00 seconds total)