Starting phenix.real_space_refine on Tue Feb 11 01:56:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc6_40339/02_2025/8sc6_40339.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc6_40339/02_2025/8sc6_40339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sc6_40339/02_2025/8sc6_40339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc6_40339/02_2025/8sc6_40339.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc6_40339/02_2025/8sc6_40339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc6_40339/02_2025/8sc6_40339.cif" } resolution = 3.13 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= 0.034 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 31 5.16 5 C 2293 2.51 5 N 565 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3479 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3461 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'VIB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.74, per 1000 atoms: 0.79 Number of scatterers: 3479 At special positions: 0 Unit cell: (90.72, 84, 68.04, 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 31 16.00 O 590 8.00 N 565 7.00 C 2293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 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: 0.89 Conformation dependent library (CDL) restraints added in 411.7 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 80.5% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.959A pdb=" N LEU A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.727A pdb=" N CYS A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 147 removed outlier: 4.520A pdb=" N TRP A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 173 removed outlier: 4.333A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.820A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.738A pdb=" N VAL A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.612A pdb=" N GLN A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 278 Proline residue: A 271 - end of helix removed outlier: 3.515A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.504A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 372 Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.508A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 398 removed outlier: 4.072A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 420 removed outlier: 3.542A pdb=" N MET A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 3.738A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 491 removed outlier: 3.788A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 3.533A pdb=" N LEU A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 removed outlier: 4.019A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 241 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 1.03 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: 1071 1.34 - 1.46: 838 1.46 - 1.58: 1616 1.58 - 1.69: 1 1.69 - 1.81: 46 Bond restraints: 3572 Sorted by residual: bond pdb=" CA LEU A 427 " pdb=" C LEU A 427 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.14e-02 7.69e+03 5.00e-01 bond pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 1.468 1.461 0.007 1.05e-02 9.07e+03 4.84e-01 bond pdb=" CA THR A 480 " pdb=" C THR A 480 " ideal model delta sigma weight residual 1.520 1.529 -0.008 1.23e-02 6.61e+03 4.75e-01 bond pdb=" C ALA A 257 " pdb=" N LEU A 258 " ideal model delta sigma weight residual 1.327 1.336 -0.009 1.32e-02 5.74e+03 4.45e-01 bond pdb=" C VAL A 461 " pdb=" O VAL A 461 " ideal model delta sigma weight residual 1.226 1.240 -0.013 2.04e-02 2.40e+03 4.30e-01 ... (remaining 3567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 4682 1.06 - 2.12: 147 2.12 - 3.17: 27 3.17 - 4.23: 7 4.23 - 5.29: 7 Bond angle restraints: 4870 Sorted by residual: angle pdb=" C GLU A 386 " pdb=" N ILE A 387 " pdb=" CA ILE A 387 " ideal model delta sigma weight residual 120.33 122.81 -2.48 8.00e-01 1.56e+00 9.59e+00 angle pdb=" C TYR A 72 " pdb=" N THR A 73 " pdb=" CA THR A 73 " ideal model delta sigma weight residual 122.46 117.60 4.86 1.80e+00 3.09e-01 7.30e+00 angle pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 114.40 119.23 -4.83 2.30e+00 1.89e-01 4.40e+00 angle pdb=" N THR A 480 " pdb=" CA THR A 480 " pdb=" C THR A 480 " ideal model delta sigma weight residual 112.75 115.58 -2.83 1.36e+00 5.41e-01 4.34e+00 angle pdb=" C VAL A 461 " pdb=" CA VAL A 461 " pdb=" CB VAL A 461 " ideal model delta sigma weight residual 112.36 109.75 2.61 1.37e+00 5.33e-01 3.62e+00 ... (remaining 4865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.01: 1882 11.01 - 22.02: 141 22.02 - 33.03: 34 33.03 - 44.04: 9 44.04 - 55.05: 1 Dihedral angle restraints: 2067 sinusoidal: 788 harmonic: 1279 Sorted by residual: dihedral pdb=" N PHE A 273 " pdb=" CA PHE A 273 " pdb=" CB PHE A 273 " pdb=" CG PHE A 273 " ideal model delta sinusoidal sigma weight residual -60.00 -115.05 55.05 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" N LEU A 150 " pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " pdb=" CG LEU A 150 " ideal model delta sinusoidal sigma weight residual -60.00 -102.93 42.93 3 1.50e+01 4.44e-03 7.71e+00 dihedral pdb=" N MET A 239 " pdb=" CA MET A 239 " pdb=" CB MET A 239 " pdb=" CG MET A 239 " ideal model delta sinusoidal sigma weight residual -180.00 -141.24 -38.76 3 1.50e+01 4.44e-03 6.84e+00 ... (remaining 2064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 313 0.022 - 0.043: 148 0.043 - 0.065: 63 0.065 - 0.087: 18 0.087 - 0.109: 20 Chirality restraints: 562 Sorted by residual: chirality pdb=" CA THR A 480 " pdb=" N THR A 480 " pdb=" C THR A 480 " pdb=" CB THR A 480 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.11 2.00e-01 2.50e+01 2.95e-01 chirality pdb=" CA LEU A 270 " pdb=" N LEU A 270 " pdb=" C LEU A 270 " pdb=" CB LEU A 270 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.88e-01 chirality pdb=" CA PRO A 53 " pdb=" N PRO A 53 " pdb=" C PRO A 53 " pdb=" CB PRO A 53 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.84e-01 ... (remaining 559 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.52e+00 pdb=" N PRO A 271 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 74 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 75 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 65 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 66 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.016 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 868 2.80 - 3.32: 3411 3.32 - 3.85: 5504 3.85 - 4.37: 6251 4.37 - 4.90: 11184 Nonbonded interactions: 27218 Sorted by model distance: nonbonded pdb=" O LYS A 147 " pdb=" OH TYR A 199 " model vdw 2.273 3.040 nonbonded pdb=" OE1 GLU A 137 " pdb=" NE1 TRP A 261 " model vdw 2.340 3.120 nonbonded pdb=" NZ LYS A 214 " pdb=" OD1 ASP A 474 " model vdw 2.351 3.120 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.353 3.040 nonbonded pdb=" O GLN A 209 " pdb=" OG SER A 213 " model vdw 2.363 3.040 ... (remaining 27213 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: 0.740 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.710 Find NCS groups from input model: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3572 Z= 0.166 Angle : 0.502 5.291 4870 Z= 0.288 Chirality : 0.035 0.109 562 Planarity : 0.004 0.031 601 Dihedral : 8.707 55.052 1240 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.81 % Allowed : 2.96 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.41), residues: 443 helix: 2.09 (0.31), residues: 302 sheet: None (None), residues: 0 loop : 1.57 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 244 TYR 0.011 0.001 TYR A 168 ARG 0.001 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.402 Fit side-chains REVERT: A 273 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: A 351 MET cc_start: 0.8709 (mtt) cc_final: 0.8385 (mtp) REVERT: A 357 ASP cc_start: 0.7980 (m-30) cc_final: 0.7731 (m-30) outliers start: 3 outliers final: 0 residues processed: 67 average time/residue: 0.1839 time to fit residues: 14.9280 Evaluate side-chains 41 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 447 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.192754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.134676 restraints weight = 3504.802| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.49 r_work: 0.3159 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3572 Z= 0.245 Angle : 0.520 6.529 4870 Z= 0.269 Chirality : 0.038 0.134 562 Planarity : 0.005 0.035 601 Dihedral : 4.832 54.719 487 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.16 % Allowed : 9.43 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.42), residues: 443 helix: 2.14 (0.30), residues: 311 sheet: None (None), residues: 0 loop : 1.33 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.005 0.001 HIS A 49 PHE 0.012 0.001 PHE A 32 TYR 0.012 0.001 TYR A 168 ARG 0.003 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.397 Fit side-chains REVERT: A 200 MET cc_start: 0.7541 (mmt) cc_final: 0.7300 (mmp) REVERT: A 273 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7580 (m-80) REVERT: A 351 MET cc_start: 0.8487 (mtt) cc_final: 0.8263 (mtm) REVERT: A 395 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6417 (mm) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.1549 time to fit residues: 9.5073 Evaluate side-chains 48 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.192893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135066 restraints weight = 3548.612| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.52 r_work: 0.3095 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3572 Z= 0.190 Angle : 0.466 5.045 4870 Z= 0.241 Chirality : 0.037 0.129 562 Planarity : 0.004 0.032 601 Dihedral : 4.722 55.931 487 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.89 % Allowed : 9.43 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.41), residues: 443 helix: 2.35 (0.30), residues: 305 sheet: None (None), residues: 0 loop : 1.32 (0.58), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.012 0.001 TYR A 168 ARG 0.002 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.371 Fit side-chains REVERT: A 200 MET cc_start: 0.7439 (mmt) cc_final: 0.7226 (mmp) REVERT: A 273 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7370 (m-80) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.1475 time to fit residues: 8.9535 Evaluate side-chains 48 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.194194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135563 restraints weight = 3526.397| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.12 r_work: 0.3106 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3572 Z= 0.175 Angle : 0.450 5.081 4870 Z= 0.233 Chirality : 0.036 0.129 562 Planarity : 0.004 0.031 601 Dihedral : 4.651 57.039 487 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.70 % Allowed : 8.89 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.41), residues: 443 helix: 2.37 (0.30), residues: 306 sheet: None (None), residues: 0 loop : 1.24 (0.58), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.012 0.001 TYR A 168 ARG 0.002 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.320 Fit side-chains REVERT: A 273 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7316 (m-80) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 0.1479 time to fit residues: 9.5896 Evaluate side-chains 49 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 12 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.194395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136063 restraints weight = 3530.362| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.11 r_work: 0.3123 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3572 Z= 0.164 Angle : 0.444 4.984 4870 Z= 0.230 Chirality : 0.036 0.128 562 Planarity : 0.004 0.030 601 Dihedral : 4.618 57.768 487 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.16 % Allowed : 10.24 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.41), residues: 443 helix: 2.42 (0.30), residues: 306 sheet: None (None), residues: 0 loop : 1.24 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.002 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.382 Fit side-chains REVERT: A 273 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7257 (m-80) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.1665 time to fit residues: 10.1915 Evaluate side-chains 48 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.0980 chunk 9 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 1 optimal weight: 0.4980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.196660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138420 restraints weight = 3605.089| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.12 r_work: 0.3159 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3572 Z= 0.121 Angle : 0.417 4.988 4870 Z= 0.216 Chirality : 0.035 0.128 562 Planarity : 0.004 0.030 601 Dihedral : 4.490 57.498 487 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.16 % Allowed : 10.78 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.42), residues: 443 helix: 2.43 (0.30), residues: 312 sheet: None (None), residues: 0 loop : 1.41 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.003 0.000 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.002 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.363 Fit side-chains REVERT: A 73 THR cc_start: 0.7851 (m) cc_final: 0.7568 (m) REVERT: A 273 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7128 (m-80) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.1464 time to fit residues: 10.0541 Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 0.0060 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.194942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136534 restraints weight = 3493.342| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.15 r_work: 0.3116 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3572 Z= 0.156 Angle : 0.455 9.766 4870 Z= 0.229 Chirality : 0.036 0.128 562 Planarity : 0.004 0.028 601 Dihedral : 4.533 58.582 487 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.43 % Allowed : 11.32 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.41), residues: 443 helix: 2.39 (0.30), residues: 311 sheet: None (None), residues: 0 loop : 1.26 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.002 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.335 Fit side-chains REVERT: A 73 THR cc_start: 0.7883 (m) cc_final: 0.7592 (m) REVERT: A 273 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7208 (m-80) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.1414 time to fit residues: 9.1752 Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.195465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137272 restraints weight = 3520.810| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.10 r_work: 0.3131 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3572 Z= 0.151 Angle : 0.448 9.205 4870 Z= 0.226 Chirality : 0.036 0.128 562 Planarity : 0.004 0.028 601 Dihedral : 4.553 59.626 487 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.43 % Allowed : 11.59 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.41), residues: 443 helix: 2.53 (0.30), residues: 305 sheet: None (None), residues: 0 loop : 1.12 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.003 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.348 Fit side-chains REVERT: A 73 THR cc_start: 0.7916 (m) cc_final: 0.7622 (m) REVERT: A 273 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7158 (m-80) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 0.1481 time to fit residues: 9.9981 Evaluate side-chains 53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 5 optimal weight: 0.0050 chunk 11 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 overall best weight: 0.2490 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.198054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.139850 restraints weight = 3496.278| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.17 r_work: 0.3168 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3572 Z= 0.108 Angle : 0.434 9.222 4870 Z= 0.217 Chirality : 0.035 0.128 562 Planarity : 0.004 0.029 601 Dihedral : 4.461 59.315 487 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.62 % Allowed : 12.67 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.41), residues: 443 helix: 2.54 (0.30), residues: 311 sheet: None (None), residues: 0 loop : 1.33 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.007 0.001 PHE A 355 TYR 0.010 0.001 TYR A 168 ARG 0.005 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.352 Fit side-chains REVERT: A 73 THR cc_start: 0.7821 (m) cc_final: 0.7530 (m) REVERT: A 273 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: A 357 ASP cc_start: 0.7655 (m-30) cc_final: 0.7315 (m-30) REVERT: A 449 ILE cc_start: 0.6722 (tt) cc_final: 0.6478 (tt) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.1383 time to fit residues: 9.7091 Evaluate side-chains 56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.194975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.136605 restraints weight = 3522.327| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.12 r_work: 0.3144 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3572 Z= 0.186 Angle : 0.473 9.141 4870 Z= 0.239 Chirality : 0.036 0.127 562 Planarity : 0.004 0.028 601 Dihedral : 4.547 59.034 487 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.89 % Allowed : 12.40 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.41), residues: 443 helix: 2.52 (0.30), residues: 311 sheet: None (None), residues: 0 loop : 1.26 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.010 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.004 0.000 ARG A 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.329 Fit side-chains REVERT: A 73 THR cc_start: 0.7873 (m) cc_final: 0.7580 (m) REVERT: A 273 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7178 (m-80) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.1497 time to fit residues: 9.7096 Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.195824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137499 restraints weight = 3556.856| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.13 r_work: 0.3139 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3572 Z= 0.150 Angle : 0.458 9.092 4870 Z= 0.230 Chirality : 0.036 0.128 562 Planarity : 0.004 0.027 601 Dihedral : 4.504 58.394 487 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.35 % Allowed : 12.67 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.41), residues: 443 helix: 2.56 (0.30), residues: 311 sheet: None (None), residues: 0 loop : 1.29 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.002 0.000 ARG A 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.97 seconds wall clock time: 43 minutes 18.66 seconds (2598.66 seconds total)