Starting phenix.real_space_refine on Wed Jun 4 22:55:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfl_37495/06_2025/8wfl_37495.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfl_37495/06_2025/8wfl_37495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wfl_37495/06_2025/8wfl_37495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfl_37495/06_2025/8wfl_37495.map" model { file = "/net/cci-nas-00/data/ceres_data/8wfl_37495/06_2025/8wfl_37495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfl_37495/06_2025/8wfl_37495.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 35 5.16 5 Cl 1 4.86 5 C 2944 2.51 5 N 695 2.21 5 O 738 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4414 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4388 Classifications: {'peptide': 552} Link IDs: {'PTRANS': 25, 'TRANS': 526} Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'W5X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.03, per 1000 atoms: 0.69 Number of scatterers: 4414 At special positions: 0 Unit cell: (85.28, 70.52, 91.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 35 16.00 F 1 9.00 O 738 8.00 N 695 7.00 C 2944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " 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: 1.04 Conformation dependent library (CDL) restraints added in 482.8 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 71.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.549A pdb=" N PHE A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 79 removed outlier: 4.803A pdb=" N PHE A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 95 through 111 Processing helix chain 'A' and resid 115 through 120 removed outlier: 4.020A pdb=" N ILE A 120 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 155 removed outlier: 4.038A pdb=" N GLY A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 233 through 251 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.599A pdb=" N THR A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Proline residue: A 269 - end of helix Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.530A pdb=" N LYS A 300 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 301 " --> pdb=" O TRP A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 301' Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.975A pdb=" N TRP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 removed outlier: 3.823A pdb=" N THR A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 372 removed outlier: 3.633A pdb=" N VAL A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 399 through 434 removed outlier: 4.257A pdb=" N TRP A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 458 Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.688A pdb=" N TRP A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 496 removed outlier: 3.774A pdb=" N VAL A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 494 " --> pdb=" O CYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 Processing helix chain 'A' and resid 515 through 524 removed outlier: 4.166A pdb=" N ILE A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 540 Processing helix chain 'A' and resid 552 through 568 removed outlier: 4.497A pdb=" N ILE A 558 " --> pdb=" O TRP A 554 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.734A pdb=" N TYR A 573 " --> pdb=" O CYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 585 through 592 Processing sheet with id=AA1, first strand: chain 'A' and resid 545 through 546 removed outlier: 4.066A pdb=" N TYR A 549 " --> pdb=" O TYR A 546 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 723 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: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 646 1.27 - 1.41: 1323 1.41 - 1.54: 2530 1.54 - 1.68: 4 1.68 - 1.82: 54 Bond restraints: 4557 Sorted by residual: bond pdb=" C14 W5X A 701 " pdb=" N04 W5X A 701 " ideal model delta sigma weight residual 1.440 1.133 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C08 W5X A 701 " pdb=" C11 W5X A 701 " ideal model delta sigma weight residual 1.512 1.330 0.182 2.00e-02 2.50e+03 8.25e+01 bond pdb=" C12 W5X A 701 " pdb=" N04 W5X A 701 " ideal model delta sigma weight residual 1.452 1.284 0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" C22 W5X A 701 " pdb=" C25 W5X A 701 " ideal model delta sigma weight residual 1.384 1.535 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" C23 W5X A 701 " pdb=" C25 W5X A 701 " ideal model delta sigma weight residual 1.381 1.525 -0.144 2.00e-02 2.50e+03 5.21e+01 ... (remaining 4552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.98: 6203 5.98 - 11.96: 12 11.96 - 17.94: 0 17.94 - 23.92: 1 23.92 - 29.90: 1 Bond angle restraints: 6217 Sorted by residual: angle pdb=" C10 W5X A 701 " pdb=" C08 W5X A 701 " pdb=" C11 W5X A 701 " ideal model delta sigma weight residual 119.35 149.25 -29.90 3.00e+00 1.11e-01 9.94e+01 angle pdb=" C10 W5X A 701 " pdb=" C09 W5X A 701 " pdb=" C12 W5X A 701 " ideal model delta sigma weight residual 121.62 140.12 -18.50 3.00e+00 1.11e-01 3.80e+01 angle pdb=" C ILE A 399 " pdb=" N SER A 400 " pdb=" CA SER A 400 " ideal model delta sigma weight residual 119.78 123.24 -3.46 1.24e+00 6.50e-01 7.78e+00 angle pdb=" CA TRP A 322 " pdb=" CB TRP A 322 " pdb=" CG TRP A 322 " ideal model delta sigma weight residual 113.60 118.64 -5.04 1.90e+00 2.77e-01 7.04e+00 angle pdb=" C15 W5X A 701 " pdb=" C17 W5X A 701 " pdb=" C19 W5X A 701 " ideal model delta sigma weight residual 120.05 112.19 7.86 3.00e+00 1.11e-01 6.87e+00 ... (remaining 6212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 2193 17.77 - 35.54: 297 35.54 - 53.32: 70 53.32 - 71.09: 17 71.09 - 88.86: 6 Dihedral angle restraints: 2583 sinusoidal: 993 harmonic: 1590 Sorted by residual: dihedral pdb=" CA PRO A 401 " pdb=" C PRO A 401 " pdb=" N LEU A 402 " pdb=" CA LEU A 402 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ALA A 321 " pdb=" C ALA A 321 " pdb=" N TRP A 322 " pdb=" CA TRP A 322 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU A 433 " pdb=" CG GLU A 433 " pdb=" CD GLU A 433 " pdb=" OE1 GLU A 433 " ideal model delta sinusoidal sigma weight residual 0.00 -88.78 88.78 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 680 0.277 - 0.553: 2 0.553 - 0.830: 1 0.830 - 1.107: 0 1.107 - 1.383: 1 Chirality restraints: 684 Sorted by residual: chirality pdb=" C08 W5X A 701 " pdb=" C09 W5X A 701 " pdb=" C10 W5X A 701 " pdb=" C11 W5X A 701 " both_signs ideal model delta sigma weight residual True 2.58 1.19 1.38 2.00e-01 2.50e+01 4.78e+01 chirality pdb=" C09 W5X A 701 " pdb=" C08 W5X A 701 " pdb=" C10 W5X A 701 " pdb=" C12 W5X A 701 " both_signs ideal model delta sigma weight residual True 2.51 -1.87 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C10 W5X A 701 " pdb=" C08 W5X A 701 " pdb=" C09 W5X A 701 " pdb=" C13 W5X A 701 " both_signs ideal model delta sigma weight residual True 2.16 2.44 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 681 not shown) Planarity restraints: 762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 170 " 0.012 2.00e-02 2.50e+03 1.26e-02 3.96e+00 pdb=" CG TRP A 170 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 170 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 170 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 170 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 170 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 170 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 170 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 170 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 170 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 86 " -0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO A 87 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 268 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 269 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.020 5.00e-02 4.00e+02 ... (remaining 759 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 816 2.76 - 3.29: 4319 3.29 - 3.83: 7361 3.83 - 4.36: 8182 4.36 - 4.90: 14212 Nonbonded interactions: 34890 Sorted by model distance: nonbonded pdb=" OG SER A 257 " pdb=" OE2 GLU A 424 " model vdw 2.223 3.040 nonbonded pdb=" O PRO A 602 " pdb=" NH2 ARG A 608 " model vdw 2.291 3.120 nonbonded pdb=" OG1 THR A 172 " pdb=" OE2 GLU A 213 " model vdw 2.311 3.040 nonbonded pdb=" CG2 VAL A 178 " pdb=" CD1 LEU A 371 " model vdw 2.312 3.880 nonbonded pdb=" OH TYR A 476 " pdb=" OH TYR A 541 " model vdw 2.326 3.040 ... (remaining 34885 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 0.009 0.307 4558 Z= 0.423 Angle : 0.807 29.903 6219 Z= 0.360 Chirality : 0.073 1.383 684 Planarity : 0.004 0.039 762 Dihedral : 17.689 88.862 1574 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.21 % Allowed : 29.98 % Favored : 69.81 % 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: -0.36 (0.37), residues: 548 helix: 0.78 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -2.20 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 170 HIS 0.003 0.001 HIS A 370 PHE 0.016 0.001 PHE A 420 TYR 0.023 0.001 TYR A 62 ARG 0.003 0.000 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.17300 ( 247) hydrogen bonds : angle 6.91702 ( 723) SS BOND : bond 0.00291 ( 1) SS BOND : angle 0.92592 ( 2) covalent geometry : bond 0.00851 ( 4557) covalent geometry : angle 0.80656 ( 6217) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.430 Fit side-chains REVERT: A 62 TYR cc_start: 0.8623 (t80) cc_final: 0.8376 (t80) REVERT: A 404 SER cc_start: 0.8489 (p) cc_final: 0.8254 (m) REVERT: A 433 GLU cc_start: 0.7952 (tp30) cc_final: 0.7305 (tt0) outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 0.1600 time to fit residues: 21.0284 Evaluate side-chains 93 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 79 ASN A 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.163836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152613 restraints weight = 6355.660| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.34 r_work: 0.3738 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4558 Z= 0.138 Angle : 0.593 5.904 6219 Z= 0.306 Chirality : 0.042 0.179 684 Planarity : 0.004 0.032 762 Dihedral : 8.884 75.307 631 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 7.07 % Allowed : 24.63 % Favored : 68.31 % 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: 0.12 (0.37), residues: 548 helix: 1.12 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -2.02 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 70 HIS 0.004 0.001 HIS A 370 PHE 0.024 0.001 PHE A 109 TYR 0.016 0.001 TYR A 141 ARG 0.003 0.000 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 247) hydrogen bonds : angle 4.55959 ( 723) SS BOND : bond 0.00494 ( 1) SS BOND : angle 1.08551 ( 2) covalent geometry : bond 0.00311 ( 4557) covalent geometry : angle 0.59261 ( 6217) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.422 Fit side-chains REVERT: A 92 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8175 (tp) REVERT: A 150 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7870 (t80) REVERT: A 433 GLU cc_start: 0.7937 (tp30) cc_final: 0.7277 (tt0) REVERT: A 516 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7661 (mt) outliers start: 33 outliers final: 23 residues processed: 116 average time/residue: 0.1494 time to fit residues: 22.2884 Evaluate side-chains 116 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.0050 chunk 31 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.164551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.153402 restraints weight = 6361.918| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.34 r_work: 0.3733 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4558 Z= 0.115 Angle : 0.553 5.634 6219 Z= 0.285 Chirality : 0.041 0.201 684 Planarity : 0.004 0.031 762 Dihedral : 8.657 75.171 631 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 7.07 % Allowed : 23.98 % Favored : 68.95 % 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: 0.23 (0.38), residues: 548 helix: 1.14 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.89 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 322 HIS 0.002 0.001 HIS A 173 PHE 0.016 0.001 PHE A 109 TYR 0.022 0.001 TYR A 141 ARG 0.005 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 247) hydrogen bonds : angle 4.25240 ( 723) SS BOND : bond 0.00398 ( 1) SS BOND : angle 1.13672 ( 2) covalent geometry : bond 0.00258 ( 4557) covalent geometry : angle 0.55309 ( 6217) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.423 Fit side-chains REVERT: A 92 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8027 (tp) REVERT: A 150 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7795 (t80) REVERT: A 314 ILE cc_start: 0.8427 (tp) cc_final: 0.8206 (tp) REVERT: A 367 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7131 (tpp) REVERT: A 424 GLU cc_start: 0.7659 (tp30) cc_final: 0.7353 (mm-30) REVERT: A 433 GLU cc_start: 0.7974 (tp30) cc_final: 0.7352 (tt0) REVERT: A 516 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7544 (mt) outliers start: 33 outliers final: 21 residues processed: 120 average time/residue: 0.1435 time to fit residues: 22.3461 Evaluate side-chains 118 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 0.0270 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.167269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.156232 restraints weight = 6341.578| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.32 r_work: 0.3759 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4558 Z= 0.110 Angle : 0.538 5.611 6219 Z= 0.278 Chirality : 0.041 0.209 684 Planarity : 0.004 0.031 762 Dihedral : 8.487 76.596 631 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.85 % Allowed : 25.05 % Favored : 68.09 % 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: 0.28 (0.38), residues: 548 helix: 1.31 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -2.08 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 70 HIS 0.002 0.000 HIS A 173 PHE 0.019 0.001 PHE A 109 TYR 0.024 0.001 TYR A 141 ARG 0.001 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 247) hydrogen bonds : angle 4.06001 ( 723) SS BOND : bond 0.00346 ( 1) SS BOND : angle 1.01960 ( 2) covalent geometry : bond 0.00245 ( 4557) covalent geometry : angle 0.53737 ( 6217) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.416 Fit side-chains REVERT: A 92 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8026 (tp) REVERT: A 129 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.6666 (m-10) REVERT: A 150 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7870 (t80) REVERT: A 278 VAL cc_start: 0.7996 (t) cc_final: 0.7795 (t) REVERT: A 424 GLU cc_start: 0.7697 (tp30) cc_final: 0.6975 (tp30) REVERT: A 433 GLU cc_start: 0.8003 (tp30) cc_final: 0.7352 (tt0) REVERT: A 516 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7551 (mt) outliers start: 32 outliers final: 21 residues processed: 108 average time/residue: 0.1331 time to fit residues: 19.1881 Evaluate side-chains 115 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.165400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.154231 restraints weight = 6475.102| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.37 r_work: 0.3753 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4558 Z= 0.113 Angle : 0.531 5.442 6219 Z= 0.273 Chirality : 0.040 0.170 684 Planarity : 0.004 0.030 762 Dihedral : 8.386 77.222 631 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 7.92 % Allowed : 23.13 % Favored : 68.95 % 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: 0.32 (0.38), residues: 548 helix: 1.33 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -2.09 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 322 HIS 0.002 0.001 HIS A 607 PHE 0.021 0.001 PHE A 109 TYR 0.021 0.001 TYR A 141 ARG 0.002 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 247) hydrogen bonds : angle 3.98908 ( 723) SS BOND : bond 0.00407 ( 1) SS BOND : angle 0.96410 ( 2) covalent geometry : bond 0.00257 ( 4557) covalent geometry : angle 0.53099 ( 6217) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.434 Fit side-chains REVERT: A 129 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.6764 (m-10) REVERT: A 150 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7954 (t80) REVERT: A 303 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: A 424 GLU cc_start: 0.7702 (tp30) cc_final: 0.7082 (tp30) REVERT: A 433 GLU cc_start: 0.7988 (tp30) cc_final: 0.7336 (tt0) REVERT: A 584 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6819 (m-30) outliers start: 37 outliers final: 24 residues processed: 113 average time/residue: 0.1406 time to fit residues: 20.9814 Evaluate side-chains 118 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.0000 chunk 11 optimal weight: 0.0000 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.167703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156524 restraints weight = 6346.642| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.30 r_work: 0.3780 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4558 Z= 0.105 Angle : 0.529 5.331 6219 Z= 0.271 Chirality : 0.039 0.154 684 Planarity : 0.004 0.030 762 Dihedral : 8.339 78.219 631 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 7.07 % Allowed : 22.91 % Favored : 70.02 % 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: 0.43 (0.38), residues: 548 helix: 1.37 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.02 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 322 HIS 0.008 0.001 HIS A 173 PHE 0.024 0.001 PHE A 109 TYR 0.021 0.001 TYR A 141 ARG 0.001 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 247) hydrogen bonds : angle 3.92826 ( 723) SS BOND : bond 0.00314 ( 1) SS BOND : angle 0.90487 ( 2) covalent geometry : bond 0.00233 ( 4557) covalent geometry : angle 0.52931 ( 6217) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 129 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.6713 (m-10) REVERT: A 303 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: A 424 GLU cc_start: 0.7738 (tp30) cc_final: 0.7191 (tp30) REVERT: A 433 GLU cc_start: 0.7901 (tp30) cc_final: 0.7251 (tt0) outliers start: 33 outliers final: 24 residues processed: 110 average time/residue: 0.1501 time to fit residues: 21.9595 Evaluate side-chains 117 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.166301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.154927 restraints weight = 6362.460| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.34 r_work: 0.3770 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4558 Z= 0.113 Angle : 0.531 5.345 6219 Z= 0.274 Chirality : 0.040 0.142 684 Planarity : 0.004 0.029 762 Dihedral : 8.263 78.535 631 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 7.07 % Allowed : 22.91 % Favored : 70.02 % 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: 0.36 (0.38), residues: 548 helix: 1.26 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -2.05 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 322 HIS 0.010 0.001 HIS A 173 PHE 0.026 0.001 PHE A 109 TYR 0.021 0.001 TYR A 141 ARG 0.003 0.000 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 247) hydrogen bonds : angle 3.90465 ( 723) SS BOND : bond 0.00445 ( 1) SS BOND : angle 0.85111 ( 2) covalent geometry : bond 0.00258 ( 4557) covalent geometry : angle 0.53068 ( 6217) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.446 Fit side-chains REVERT: A 129 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.6759 (m-10) REVERT: A 303 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: A 424 GLU cc_start: 0.7741 (tp30) cc_final: 0.7203 (tp30) REVERT: A 433 GLU cc_start: 0.7884 (tp30) cc_final: 0.7231 (tt0) outliers start: 33 outliers final: 26 residues processed: 111 average time/residue: 0.1403 time to fit residues: 20.5684 Evaluate side-chains 118 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.163305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151529 restraints weight = 6345.799| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.46 r_work: 0.3763 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4558 Z= 0.119 Angle : 0.539 5.312 6219 Z= 0.277 Chirality : 0.041 0.136 684 Planarity : 0.004 0.028 762 Dihedral : 8.186 78.584 631 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.42 % Allowed : 23.98 % Favored : 69.59 % 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: 0.40 (0.38), residues: 548 helix: 1.22 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.97 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 322 HIS 0.010 0.001 HIS A 173 PHE 0.029 0.001 PHE A 109 TYR 0.024 0.001 TYR A 141 ARG 0.002 0.000 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 247) hydrogen bonds : angle 3.92354 ( 723) SS BOND : bond 0.00451 ( 1) SS BOND : angle 0.87254 ( 2) covalent geometry : bond 0.00278 ( 4557) covalent geometry : angle 0.53920 ( 6217) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.606 Fit side-chains REVERT: A 129 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.6795 (m-10) REVERT: A 303 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: A 424 GLU cc_start: 0.7737 (tp30) cc_final: 0.7202 (tp30) REVERT: A 433 GLU cc_start: 0.7932 (tp30) cc_final: 0.7204 (tt0) outliers start: 30 outliers final: 26 residues processed: 106 average time/residue: 0.2629 time to fit residues: 37.1207 Evaluate side-chains 115 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.163722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.152370 restraints weight = 6428.054| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.35 r_work: 0.3723 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4558 Z= 0.130 Angle : 0.552 5.458 6219 Z= 0.282 Chirality : 0.041 0.134 684 Planarity : 0.004 0.028 762 Dihedral : 8.147 78.613 631 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.64 % Allowed : 23.55 % Favored : 69.81 % 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: 0.34 (0.38), residues: 548 helix: 1.24 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -2.06 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 600 HIS 0.010 0.001 HIS A 173 PHE 0.030 0.001 PHE A 109 TYR 0.022 0.001 TYR A 141 ARG 0.002 0.000 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 247) hydrogen bonds : angle 3.96123 ( 723) SS BOND : bond 0.00554 ( 1) SS BOND : angle 0.90248 ( 2) covalent geometry : bond 0.00302 ( 4557) covalent geometry : angle 0.55179 ( 6217) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.557 Fit side-chains REVERT: A 129 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.6846 (m-10) REVERT: A 422 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8660 (mp) REVERT: A 424 GLU cc_start: 0.7733 (tp30) cc_final: 0.7207 (tp30) REVERT: A 433 GLU cc_start: 0.7920 (tp30) cc_final: 0.7228 (tt0) REVERT: A 440 LEU cc_start: 0.6974 (mm) cc_final: 0.6723 (mm) outliers start: 31 outliers final: 26 residues processed: 112 average time/residue: 0.1399 time to fit residues: 20.8072 Evaluate side-chains 119 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 33 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.168297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.157082 restraints weight = 6085.238| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.26 r_work: 0.3788 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4558 Z= 0.110 Angle : 0.548 6.624 6219 Z= 0.280 Chirality : 0.041 0.194 684 Planarity : 0.004 0.029 762 Dihedral : 8.110 79.485 631 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 6.42 % Allowed : 24.63 % Favored : 68.95 % 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: 0.39 (0.38), residues: 548 helix: 1.28 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -2.06 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 600 HIS 0.002 0.000 HIS A 607 PHE 0.030 0.001 PHE A 109 TYR 0.022 0.001 TYR A 141 ARG 0.001 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 247) hydrogen bonds : angle 3.98930 ( 723) SS BOND : bond 0.00366 ( 1) SS BOND : angle 0.90531 ( 2) covalent geometry : bond 0.00247 ( 4557) covalent geometry : angle 0.54802 ( 6217) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.464 Fit side-chains REVERT: A 119 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.8075 (mtp85) REVERT: A 129 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.6795 (m-10) REVERT: A 303 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: A 422 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8656 (mp) REVERT: A 424 GLU cc_start: 0.7720 (tp30) cc_final: 0.7239 (tp30) REVERT: A 433 GLU cc_start: 0.7882 (tp30) cc_final: 0.7210 (tt0) REVERT: A 440 LEU cc_start: 0.6926 (mm) cc_final: 0.6679 (mm) outliers start: 30 outliers final: 25 residues processed: 106 average time/residue: 0.1285 time to fit residues: 18.0611 Evaluate side-chains 117 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 0.3980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.165109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.152983 restraints weight = 6277.946| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.51 r_work: 0.3744 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4558 Z= 0.109 Angle : 0.540 7.171 6219 Z= 0.275 Chirality : 0.041 0.154 684 Planarity : 0.004 0.030 762 Dihedral : 8.047 80.302 631 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 6.42 % Allowed : 24.84 % Favored : 68.74 % 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: 0.50 (0.38), residues: 548 helix: 1.38 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -2.03 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 600 HIS 0.008 0.001 HIS A 173 PHE 0.028 0.001 PHE A 109 TYR 0.022 0.001 TYR A 141 ARG 0.001 0.000 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 247) hydrogen bonds : angle 3.95342 ( 723) SS BOND : bond 0.00387 ( 1) SS BOND : angle 0.86020 ( 2) covalent geometry : bond 0.00250 ( 4557) covalent geometry : angle 0.53990 ( 6217) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2682.28 seconds wall clock time: 48 minutes 22.65 seconds (2902.65 seconds total)