Starting phenix.real_space_refine on Wed Mar 5 22:21:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zh0_14716/03_2025/7zh0_14716.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh0_14716/03_2025/7zh0_14716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zh0_14716/03_2025/7zh0_14716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh0_14716/03_2025/7zh0_14716.map" model { file = "/net/cci-nas-00/data/ceres_data/7zh0_14716/03_2025/7zh0_14716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh0_14716/03_2025/7zh0_14716.cif" } resolution = 3.2 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= 0.001 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 22 5.16 5 C 2557 2.51 5 N 640 2.21 5 O 650 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-5624/modules/chem_data/mon_lib" Total number of atoms: 3869 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3869 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 23, 'TRANS': 471} Chain breaks: 3 Time building chain proxies: 3.23, per 1000 atoms: 0.83 Number of scatterers: 3869 At special positions: 0 Unit cell: (102.3, 63.36, 75.9, 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 22 16.00 O 650 8.00 N 640 7.00 C 2557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 148 " 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: 1.03 Conformation dependent library (CDL) restraints added in 498.9 milliseconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 80.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.620A pdb=" N THR A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 42 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 94 through 99 removed outlier: 4.162A pdb=" N ALA A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.614A pdb=" N TRP A 152 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 179 removed outlier: 3.835A pdb=" N THR A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 removed outlier: 3.629A pdb=" N ILE A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 234 removed outlier: 3.970A pdb=" N GLY A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 264 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.776A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.575A pdb=" N VAL A 288 " --> pdb=" O TYR A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.577A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.641A pdb=" N VAL A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 373 removed outlier: 3.655A pdb=" N GLY A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 389 through 405 removed outlier: 4.637A pdb=" N GLY A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 426 Processing helix chain 'A' and resid 433 through 461 removed outlier: 4.268A pdb=" N THR A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 471 through 495 Proline residue: A 485 - end of helix removed outlier: 3.669A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.859A pdb=" N ASP A 531 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 93 262 hydrogen bonds defined for protein. 768 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: 1.05 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1196 1.34 - 1.46: 633 1.46 - 1.57: 2106 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3965 Sorted by residual: bond pdb=" N PHE A 450 " pdb=" CA PHE A 450 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.35e+00 bond pdb=" N MET A 448 " pdb=" CA MET A 448 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.10e+00 bond pdb=" N GLU A 451 " pdb=" CA GLU A 451 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 4.96e+00 bond pdb=" N ALA A 449 " pdb=" CA ALA A 449 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.67e+00 bond pdb=" N THR A 528 " pdb=" CA THR A 528 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.24e+00 ... (remaining 3960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 5075 1.31 - 2.61: 234 2.61 - 3.92: 64 3.92 - 5.22: 15 5.22 - 6.53: 9 Bond angle restraints: 5397 Sorted by residual: angle pdb=" N MET A 448 " pdb=" CA MET A 448 " pdb=" C MET A 448 " ideal model delta sigma weight residual 111.28 107.52 3.76 1.09e+00 8.42e-01 1.19e+01 angle pdb=" C VAL A 470 " pdb=" N SER A 471 " pdb=" CA SER A 471 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" N VAL A 529 " pdb=" CA VAL A 529 " pdb=" C VAL A 529 " ideal model delta sigma weight residual 112.80 109.18 3.62 1.15e+00 7.56e-01 9.90e+00 angle pdb=" C GLU A 13 " pdb=" CA GLU A 13 " pdb=" CB GLU A 13 " ideal model delta sigma weight residual 110.42 116.48 -6.06 1.99e+00 2.53e-01 9.27e+00 angle pdb=" C THR A 297 " pdb=" N ARG A 298 " pdb=" CA ARG A 298 " ideal model delta sigma weight residual 123.91 128.84 -4.93 1.66e+00 3.63e-01 8.82e+00 ... (remaining 5392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 2089 17.90 - 35.79: 161 35.79 - 53.69: 39 53.69 - 71.58: 5 71.58 - 89.48: 4 Dihedral angle restraints: 2298 sinusoidal: 895 harmonic: 1403 Sorted by residual: dihedral pdb=" CA VAL A 532 " pdb=" C VAL A 532 " pdb=" N GLU A 533 " pdb=" CA GLU A 533 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.92e+00 dihedral pdb=" N PHE A 450 " pdb=" CA PHE A 450 " pdb=" CB PHE A 450 " pdb=" CG PHE A 450 " ideal model delta sinusoidal sigma weight residual -60.00 -118.37 58.37 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET A 448 " pdb=" CG MET A 448 " pdb=" SD MET A 448 " pdb=" CE MET A 448 " ideal model delta sinusoidal sigma weight residual 60.00 1.88 58.12 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 427 0.038 - 0.076: 149 0.076 - 0.114: 46 0.114 - 0.151: 3 0.151 - 0.189: 4 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA PHE A 450 " pdb=" N PHE A 450 " pdb=" C PHE A 450 " pdb=" CB PHE A 450 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CA MET A 448 " pdb=" N MET A 448 " pdb=" C MET A 448 " pdb=" CB MET A 448 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CB ILE A 523 " pdb=" CA ILE A 523 " pdb=" CG1 ILE A 523 " pdb=" CG2 ILE A 523 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 626 not shown) Planarity restraints: 669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 291 " -0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 292 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 519 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C GLU A 519 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU A 519 " -0.012 2.00e-02 2.50e+03 pdb=" N THR A 520 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 131 " 0.010 2.00e-02 2.50e+03 9.61e-03 2.31e+00 pdb=" CG TRP A 131 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 131 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 131 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 131 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 131 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 131 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 131 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 131 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 131 " 0.000 2.00e-02 2.50e+03 ... (remaining 666 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 240 2.73 - 3.27: 4304 3.27 - 3.82: 6583 3.82 - 4.36: 7315 4.36 - 4.90: 12549 Nonbonded interactions: 30991 Sorted by model distance: nonbonded pdb=" OG1 THR A 28 " pdb=" OH TYR A 185 " model vdw 2.191 3.040 nonbonded pdb=" O CYS A 189 " pdb=" OG SER A 278 " model vdw 2.244 3.040 nonbonded pdb=" OE2 GLU A 232 " pdb=" NH1 ARG A 466 " model vdw 2.254 3.120 nonbonded pdb=" N ARG A 406 " pdb=" OE2 GLU A 519 " model vdw 2.293 3.120 nonbonded pdb=" NE ARG A 178 " pdb=" OD1 ASN A 335 " model vdw 2.296 3.120 ... (remaining 30986 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: 1.750 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.430 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3965 Z= 0.250 Angle : 0.719 6.530 5397 Z= 0.394 Chirality : 0.043 0.189 629 Planarity : 0.005 0.082 669 Dihedral : 13.972 89.476 1394 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.51 % 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: 1.08 (0.39), residues: 487 helix: 1.50 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.47 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 131 HIS 0.002 0.001 HIS A 137 PHE 0.025 0.002 PHE A 410 TYR 0.009 0.001 TYR A 133 ARG 0.003 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.389 Fit side-chains REVERT: A 306 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 478 ASP cc_start: 0.7985 (m-30) cc_final: 0.7611 (m-30) REVERT: A 515 MET cc_start: 0.6321 (ttm) cc_final: 0.5736 (mmp) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1571 time to fit residues: 15.9914 Evaluate side-chains 59 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.140584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.120295 restraints weight = 6709.839| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.03 r_work: 0.3675 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3965 Z= 0.232 Angle : 0.640 5.921 5397 Z= 0.328 Chirality : 0.041 0.136 629 Planarity : 0.005 0.068 669 Dihedral : 4.429 16.774 536 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.71 % Allowed : 13.20 % Favored : 85.09 % 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: 1.34 (0.39), residues: 487 helix: 1.76 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.41 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 65 HIS 0.003 0.001 HIS A 137 PHE 0.013 0.001 PHE A 450 TYR 0.013 0.001 TYR A 185 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.426 Fit side-chains REVERT: A 179 TYR cc_start: 0.7457 (m-10) cc_final: 0.7212 (m-10) REVERT: A 435 ARG cc_start: 0.7287 (mmt90) cc_final: 0.6929 (tpt-90) REVERT: A 478 ASP cc_start: 0.8058 (m-30) cc_final: 0.7641 (m-30) REVERT: A 515 MET cc_start: 0.6664 (ttm) cc_final: 0.6020 (mmp) outliers start: 7 outliers final: 6 residues processed: 72 average time/residue: 0.1429 time to fit residues: 13.4375 Evaluate side-chains 65 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.142047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.121873 restraints weight = 6683.290| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.00 r_work: 0.3699 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3965 Z= 0.205 Angle : 0.613 7.331 5397 Z= 0.314 Chirality : 0.040 0.124 629 Planarity : 0.005 0.058 669 Dihedral : 4.325 17.374 536 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.69 % Allowed : 16.14 % Favored : 81.17 % 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: 1.29 (0.39), residues: 487 helix: 1.68 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.36 (0.50), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 65 HIS 0.002 0.001 HIS A 137 PHE 0.010 0.001 PHE A 450 TYR 0.006 0.001 TYR A 49 ARG 0.002 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.394 Fit side-chains REVERT: A 14 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8860 (m-80) REVERT: A 459 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: A 478 ASP cc_start: 0.8113 (m-30) cc_final: 0.7703 (m-30) REVERT: A 515 MET cc_start: 0.6631 (ttm) cc_final: 0.5996 (mmp) outliers start: 11 outliers final: 8 residues processed: 78 average time/residue: 0.1220 time to fit residues: 12.5824 Evaluate side-chains 73 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.0670 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.141585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.121667 restraints weight = 6748.662| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.05 r_work: 0.3699 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3965 Z= 0.206 Angle : 0.608 7.825 5397 Z= 0.311 Chirality : 0.040 0.139 629 Planarity : 0.005 0.057 669 Dihedral : 4.268 16.427 536 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.42 % Allowed : 18.83 % Favored : 77.75 % 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: 1.25 (0.39), residues: 487 helix: 1.65 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.32 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.002 0.001 HIS A 137 PHE 0.010 0.001 PHE A 384 TYR 0.006 0.001 TYR A 49 ARG 0.001 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.438 Fit side-chains REVERT: A 14 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8844 (m-80) REVERT: A 133 TYR cc_start: 0.8424 (m-80) cc_final: 0.8208 (m-80) REVERT: A 140 ILE cc_start: 0.7818 (pt) cc_final: 0.7437 (pt) REVERT: A 177 ASP cc_start: 0.7400 (t70) cc_final: 0.7055 (t70) REVERT: A 384 PHE cc_start: 0.7914 (t80) cc_final: 0.7357 (t80) REVERT: A 435 ARG cc_start: 0.7314 (tpt-90) cc_final: 0.6997 (tpt-90) REVERT: A 459 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: A 478 ASP cc_start: 0.8158 (m-30) cc_final: 0.7732 (m-30) REVERT: A 515 MET cc_start: 0.6690 (ttm) cc_final: 0.6057 (mmp) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 0.1202 time to fit residues: 13.2754 Evaluate side-chains 73 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN A 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.137363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.116950 restraints weight = 7012.005| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.12 r_work: 0.3628 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3965 Z= 0.271 Angle : 0.639 8.143 5397 Z= 0.332 Chirality : 0.041 0.162 629 Planarity : 0.005 0.053 669 Dihedral : 4.427 17.004 536 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.65 % Allowed : 18.83 % Favored : 76.53 % 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: 1.11 (0.38), residues: 487 helix: 1.48 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.23 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 152 HIS 0.006 0.002 HIS A 137 PHE 0.011 0.002 PHE A 410 TYR 0.026 0.002 TYR A 365 ARG 0.002 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.391 Fit side-chains REVERT: A 14 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8786 (m-80) REVERT: A 140 ILE cc_start: 0.7989 (pt) cc_final: 0.7741 (pt) REVERT: A 177 ASP cc_start: 0.7483 (t70) cc_final: 0.7168 (t70) REVERT: A 384 PHE cc_start: 0.7905 (t80) cc_final: 0.7362 (t80) REVERT: A 435 ARG cc_start: 0.7432 (tpt-90) cc_final: 0.7167 (tpt-90) REVERT: A 459 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: A 478 ASP cc_start: 0.8189 (m-30) cc_final: 0.7798 (m-30) REVERT: A 515 MET cc_start: 0.6812 (ttm) cc_final: 0.6297 (mmp) outliers start: 19 outliers final: 12 residues processed: 85 average time/residue: 0.1094 time to fit residues: 12.4379 Evaluate side-chains 78 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 0.0040 chunk 8 optimal weight: 0.0370 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 0.4270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.141897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.121554 restraints weight = 6791.925| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.05 r_work: 0.3698 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3965 Z= 0.192 Angle : 0.613 7.402 5397 Z= 0.313 Chirality : 0.040 0.148 629 Planarity : 0.005 0.053 669 Dihedral : 4.253 16.525 536 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.13 % Allowed : 20.54 % Favored : 74.33 % 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: 1.14 (0.39), residues: 487 helix: 1.57 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.38 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.003 0.001 HIS A 137 PHE 0.009 0.001 PHE A 384 TYR 0.013 0.001 TYR A 133 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.404 Fit side-chains REVERT: A 14 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8891 (m-80) REVERT: A 384 PHE cc_start: 0.7883 (t80) cc_final: 0.7347 (t80) REVERT: A 459 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: A 478 ASP cc_start: 0.8191 (m-30) cc_final: 0.7785 (m-30) REVERT: A 515 MET cc_start: 0.6665 (ttm) cc_final: 0.6233 (mmp) outliers start: 21 outliers final: 14 residues processed: 89 average time/residue: 0.1282 time to fit residues: 15.0488 Evaluate side-chains 79 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 0.0050 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.5032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.141275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.121199 restraints weight = 6802.547| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 3.05 r_work: 0.3690 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3965 Z= 0.206 Angle : 0.621 9.089 5397 Z= 0.319 Chirality : 0.040 0.143 629 Planarity : 0.005 0.052 669 Dihedral : 4.225 15.765 536 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.89 % Allowed : 22.25 % Favored : 72.86 % 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: 1.16 (0.39), residues: 487 helix: 1.61 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -1.41 (0.49), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.003 0.001 HIS A 137 PHE 0.008 0.001 PHE A 450 TYR 0.014 0.001 TYR A 179 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.394 Fit side-chains REVERT: A 14 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8881 (m-80) REVERT: A 384 PHE cc_start: 0.7812 (t80) cc_final: 0.7257 (t80) REVERT: A 459 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: A 478 ASP cc_start: 0.8213 (m-30) cc_final: 0.7813 (m-30) REVERT: A 515 MET cc_start: 0.6745 (ttm) cc_final: 0.6299 (mmp) outliers start: 20 outliers final: 16 residues processed: 84 average time/residue: 0.1273 time to fit residues: 13.8989 Evaluate side-chains 82 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.141342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.121256 restraints weight = 6728.177| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.11 r_work: 0.3685 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3965 Z= 0.212 Angle : 0.628 9.134 5397 Z= 0.322 Chirality : 0.040 0.135 629 Planarity : 0.005 0.052 669 Dihedral : 4.251 16.001 536 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.13 % Allowed : 22.74 % Favored : 72.13 % 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: 1.16 (0.38), residues: 487 helix: 1.61 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.43 (0.49), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 65 HIS 0.003 0.001 HIS A 137 PHE 0.009 0.001 PHE A 503 TYR 0.005 0.001 TYR A 49 ARG 0.005 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.426 Fit side-chains REVERT: A 14 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8897 (m-80) REVERT: A 384 PHE cc_start: 0.7813 (t80) cc_final: 0.7251 (t80) REVERT: A 459 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: A 478 ASP cc_start: 0.8208 (m-30) cc_final: 0.7826 (m-30) REVERT: A 515 MET cc_start: 0.6733 (ttm) cc_final: 0.6326 (mmp) outliers start: 21 outliers final: 16 residues processed: 88 average time/residue: 0.1306 time to fit residues: 14.9970 Evaluate side-chains 82 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 43 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.140616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.120941 restraints weight = 6766.252| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.04 r_work: 0.3682 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3965 Z= 0.219 Angle : 0.636 9.247 5397 Z= 0.327 Chirality : 0.041 0.147 629 Planarity : 0.005 0.052 669 Dihedral : 4.286 15.889 536 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.65 % Allowed : 22.74 % Favored : 72.62 % 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: 1.11 (0.38), residues: 487 helix: 1.57 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.42 (0.49), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 65 HIS 0.003 0.001 HIS A 137 PHE 0.010 0.001 PHE A 22 TYR 0.015 0.001 TYR A 179 ARG 0.004 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.469 Fit side-chains REVERT: A 14 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8854 (m-80) REVERT: A 384 PHE cc_start: 0.7822 (t80) cc_final: 0.7264 (t80) REVERT: A 459 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: A 478 ASP cc_start: 0.8214 (m-30) cc_final: 0.7825 (m-30) REVERT: A 515 MET cc_start: 0.6725 (ttm) cc_final: 0.6388 (mmp) outliers start: 19 outliers final: 17 residues processed: 85 average time/residue: 0.1346 time to fit residues: 15.0757 Evaluate side-chains 82 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.142094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122063 restraints weight = 6810.790| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.07 r_work: 0.3699 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3965 Z= 0.197 Angle : 0.623 9.335 5397 Z= 0.322 Chirality : 0.040 0.147 629 Planarity : 0.005 0.053 669 Dihedral : 4.236 15.545 536 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.89 % Allowed : 22.98 % Favored : 72.13 % 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: 1.12 (0.38), residues: 487 helix: 1.58 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.45 (0.49), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 65 HIS 0.003 0.001 HIS A 137 PHE 0.010 0.001 PHE A 503 TYR 0.008 0.001 TYR A 454 ARG 0.004 0.000 ARG A 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.403 Fit side-chains REVERT: A 14 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8868 (m-80) REVERT: A 384 PHE cc_start: 0.7747 (t80) cc_final: 0.7199 (t80) REVERT: A 459 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 478 ASP cc_start: 0.8152 (m-30) cc_final: 0.7784 (m-30) REVERT: A 515 MET cc_start: 0.6766 (ttm) cc_final: 0.6448 (mmp) outliers start: 20 outliers final: 18 residues processed: 86 average time/residue: 0.1295 time to fit residues: 14.8778 Evaluate side-chains 83 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.137341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.117226 restraints weight = 6815.797| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.07 r_work: 0.3636 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3965 Z= 0.257 Angle : 0.659 9.119 5397 Z= 0.342 Chirality : 0.042 0.172 629 Planarity : 0.005 0.055 669 Dihedral : 4.420 15.874 536 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.89 % Allowed : 22.49 % Favored : 72.62 % 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: 0.95 (0.38), residues: 487 helix: 1.45 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -1.45 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 65 HIS 0.003 0.001 HIS A 137 PHE 0.013 0.002 PHE A 356 TYR 0.015 0.002 TYR A 179 ARG 0.004 0.000 ARG A 435 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2392.31 seconds wall clock time: 41 minutes 46.24 seconds (2506.24 seconds total)