Starting phenix.real_space_refine on Fri Aug 22 14:48:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfl_37495/08_2025/8wfl_37495.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfl_37495/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wfl_37495/08_2025/8wfl_37495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfl_37495/08_2025/8wfl_37495.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wfl_37495/08_2025/8wfl_37495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfl_37495/08_2025/8wfl_37495.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.40, per 1000 atoms: 0.32 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: 0.40 Conformation dependent library (CDL) restraints added in 150.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.15 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: 0.65 Time building geometry restraints manager: 0.51 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.000 Find NCS groups from input model: 0.010 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: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.100 ------------------------------------------------------------------------------- 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 : 10.93 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 119 TYR 0.023 0.001 TYR A 62 PHE 0.016 0.001 PHE A 420 TRP 0.033 0.002 TRP A 170 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00851 ( 4557) covalent geometry : angle 0.80656 ( 6217) SS BOND : bond 0.00291 ( 1) SS BOND : angle 0.92592 ( 2) hydrogen bonds : bond 0.17300 ( 247) hydrogen bonds : angle 6.91702 ( 723) *********************** 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 : 0.118 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: 0.0695 time to fit residues: 9.1528 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 : 0.123 ------------------------------------------------------------------------------- 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 54 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.159425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148225 restraints weight = 6531.515| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.31 r_work: 0.3685 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4558 Z= 0.227 Angle : 0.666 6.603 6219 Z= 0.345 Chirality : 0.046 0.185 684 Planarity : 0.005 0.035 762 Dihedral : 8.901 73.442 631 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 8.78 % Allowed : 22.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.37), residues: 548 helix: 0.83 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -2.09 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 589 TYR 0.016 0.001 TYR A 141 PHE 0.029 0.002 PHE A 109 TRP 0.020 0.002 TRP A 70 HIS 0.005 0.002 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 4557) covalent geometry : angle 0.66533 ( 6217) SS BOND : bond 0.00901 ( 1) SS BOND : angle 1.29000 ( 2) hydrogen bonds : bond 0.05409 ( 247) hydrogen bonds : angle 4.65184 ( 723) *********************** 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 143 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 102 time to evaluate : 0.133 Fit side-chains REVERT: A 92 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8194 (tp) REVERT: A 150 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7990 (t80) REVERT: A 404 SER cc_start: 0.8450 (p) cc_final: 0.8214 (m) REVERT: A 433 GLU cc_start: 0.8026 (tp30) cc_final: 0.7313 (tt0) REVERT: A 516 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7865 (mt) outliers start: 41 outliers final: 27 residues processed: 120 average time/residue: 0.0605 time to fit residues: 9.3612 Evaluate side-chains 125 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 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 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 494 MET Chi-restraints excluded: chain A residue 496 ILE 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 4 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.162749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151807 restraints weight = 6340.174| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.28 r_work: 0.3717 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1210 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= 0.126 Angle : 0.573 6.073 6219 Z= 0.297 Chirality : 0.042 0.206 684 Planarity : 0.004 0.031 762 Dihedral : 8.673 74.022 631 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 7.07 % Allowed : 23.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.37), residues: 548 helix: 1.02 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.92 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.018 0.001 TYR A 141 PHE 0.015 0.001 PHE A 109 TRP 0.017 0.001 TRP A 322 HIS 0.003 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4557) covalent geometry : angle 0.57271 ( 6217) SS BOND : bond 0.00512 ( 1) SS BOND : angle 1.18739 ( 2) hydrogen bonds : bond 0.04562 ( 247) hydrogen bonds : angle 4.33835 ( 723) *********************** 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 135 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.124 Fit side-chains REVERT: A 92 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8086 (tp) REVERT: A 129 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6687 (m-10) REVERT: A 150 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7953 (t80) REVERT: A 314 ILE cc_start: 0.8440 (tp) cc_final: 0.8228 (tp) REVERT: A 327 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8088 (m) REVERT: A 367 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7055 (tpp) REVERT: A 404 SER cc_start: 0.8366 (p) cc_final: 0.8118 (m) REVERT: A 424 GLU cc_start: 0.7657 (tp30) cc_final: 0.7340 (mm-30) REVERT: A 433 GLU cc_start: 0.8001 (tp30) cc_final: 0.7339 (tt0) REVERT: A 516 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7705 (mt) outliers start: 33 outliers final: 22 residues processed: 118 average time/residue: 0.0586 time to fit residues: 9.0425 Evaluate side-chains 123 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 75 LEU 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 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 327 THR 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 332 ASN A 336 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.159254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148233 restraints weight = 6378.866| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.31 r_work: 0.3677 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4558 Z= 0.178 Angle : 0.610 6.321 6219 Z= 0.316 Chirality : 0.044 0.196 684 Planarity : 0.004 0.033 762 Dihedral : 8.559 73.454 631 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 8.57 % Allowed : 23.55 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.37), residues: 548 helix: 0.94 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -1.99 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 611 TYR 0.025 0.001 TYR A 141 PHE 0.017 0.001 PHE A 109 TRP 0.019 0.002 TRP A 322 HIS 0.004 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 4557) covalent geometry : angle 0.61012 ( 6217) SS BOND : bond 0.00785 ( 1) SS BOND : angle 1.18325 ( 2) hydrogen bonds : bond 0.04694 ( 247) hydrogen bonds : angle 4.26439 ( 723) *********************** 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 138 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.168 Fit side-chains REVERT: A 129 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.6784 (m-10) REVERT: A 150 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8019 (t80) REVERT: A 327 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8286 (m) REVERT: A 367 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7121 (tpp) REVERT: A 404 SER cc_start: 0.8384 (p) cc_final: 0.8139 (m) REVERT: A 424 GLU cc_start: 0.7667 (tp30) cc_final: 0.6852 (tp30) REVERT: A 433 GLU cc_start: 0.8046 (tp30) cc_final: 0.7371 (tt0) REVERT: A 516 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7823 (mt) outliers start: 40 outliers final: 26 residues processed: 119 average time/residue: 0.0545 time to fit residues: 8.6088 Evaluate side-chains 124 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 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 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 294 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 360 ILE 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 496 ILE 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 25 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN A 336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.162128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151335 restraints weight = 6380.871| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.26 r_work: 0.3705 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1534 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= 0.124 Angle : 0.572 6.043 6219 Z= 0.295 Chirality : 0.041 0.172 684 Planarity : 0.004 0.030 762 Dihedral : 8.486 75.122 631 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 9.21 % Allowed : 22.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.38), residues: 548 helix: 1.06 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.87 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.025 0.001 TYR A 141 PHE 0.020 0.001 PHE A 109 TRP 0.017 0.001 TRP A 322 HIS 0.002 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4557) covalent geometry : angle 0.57211 ( 6217) SS BOND : bond 0.00469 ( 1) SS BOND : angle 1.05039 ( 2) hydrogen bonds : bond 0.04267 ( 247) hydrogen bonds : angle 4.12626 ( 723) *********************** 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 137 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 94 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 129 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.6741 (m-10) REVERT: A 150 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8047 (t80) REVERT: A 251 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7775 (tp) REVERT: A 303 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: A 327 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8154 (m) REVERT: A 404 SER cc_start: 0.8376 (p) cc_final: 0.8101 (m) REVERT: A 424 GLU cc_start: 0.7630 (tp30) cc_final: 0.6935 (tp30) REVERT: A 433 GLU cc_start: 0.8016 (tp30) cc_final: 0.7390 (tt0) REVERT: A 516 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7644 (mt) outliers start: 43 outliers final: 31 residues processed: 119 average time/residue: 0.0623 time to fit residues: 9.7780 Evaluate side-chains 128 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 104 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 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 251 LEU 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 312 SER Chi-restraints excluded: chain A residue 327 THR 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 461 LEU 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 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 26 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.152404 restraints weight = 6504.887| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.35 r_work: 0.3710 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1657 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= 0.116 Angle : 0.549 5.475 6219 Z= 0.284 Chirality : 0.041 0.155 684 Planarity : 0.004 0.031 762 Dihedral : 8.372 76.846 631 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 7.92 % Allowed : 24.63 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.38), residues: 548 helix: 1.16 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.79 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 608 TYR 0.034 0.001 TYR A 293 PHE 0.025 0.001 PHE A 109 TRP 0.018 0.001 TRP A 322 HIS 0.006 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4557) covalent geometry : angle 0.54932 ( 6217) SS BOND : bond 0.00451 ( 1) SS BOND : angle 0.89288 ( 2) hydrogen bonds : bond 0.04033 ( 247) hydrogen bonds : angle 4.04764 ( 723) *********************** 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 132 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 129 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6776 (m-10) REVERT: A 150 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.8063 (t80) REVERT: A 251 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7788 (tp) REVERT: A 291 MET cc_start: 0.7364 (mpt) cc_final: 0.7148 (mpt) REVERT: A 424 GLU cc_start: 0.7704 (tp30) cc_final: 0.7099 (tp30) REVERT: A 433 GLU cc_start: 0.7970 (tp30) cc_final: 0.7337 (tt0) REVERT: A 516 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7755 (mt) outliers start: 37 outliers final: 29 residues processed: 114 average time/residue: 0.0556 time to fit residues: 8.3463 Evaluate side-chains 124 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 104 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 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 251 LEU 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 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 461 LEU 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 Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 540 GLN 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 = 0.163421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.152240 restraints weight = 6453.044| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.34 r_work: 0.3698 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4558 Z= 0.120 Angle : 0.556 5.794 6219 Z= 0.288 Chirality : 0.040 0.144 684 Planarity : 0.004 0.034 762 Dihedral : 8.312 77.317 631 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 8.14 % Allowed : 25.27 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.38), residues: 548 helix: 1.25 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.87 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 119 TYR 0.031 0.001 TYR A 293 PHE 0.025 0.001 PHE A 109 TRP 0.015 0.001 TRP A 322 HIS 0.008 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4557) covalent geometry : angle 0.55592 ( 6217) SS BOND : bond 0.00462 ( 1) SS BOND : angle 0.94095 ( 2) hydrogen bonds : bond 0.04014 ( 247) hydrogen bonds : angle 4.03063 ( 723) *********************** 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 131 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 0.139 Fit side-chains REVERT: A 129 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6787 (m-10) REVERT: A 150 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8096 (t80) REVERT: A 251 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7802 (tp) REVERT: A 291 MET cc_start: 0.7273 (mpt) cc_final: 0.7033 (mpt) REVERT: A 327 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8022 (m) REVERT: A 424 GLU cc_start: 0.7687 (tp30) cc_final: 0.7107 (tp30) REVERT: A 433 GLU cc_start: 0.7994 (tp30) cc_final: 0.7341 (tt0) REVERT: A 516 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7724 (mt) REVERT: A 584 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6806 (m-30) outliers start: 38 outliers final: 28 residues processed: 112 average time/residue: 0.0559 time to fit residues: 8.4396 Evaluate side-chains 125 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 104 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 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 251 LEU 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 327 THR 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 461 LEU 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 584 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 14 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.164202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.153175 restraints weight = 6392.219| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.28 r_work: 0.3708 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1765 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= 0.120 Angle : 0.546 5.507 6219 Z= 0.282 Chirality : 0.040 0.138 684 Planarity : 0.004 0.030 762 Dihedral : 8.208 77.736 631 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 8.35 % Allowed : 24.63 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.38), residues: 548 helix: 1.18 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.94 (0.50), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 119 TYR 0.028 0.001 TYR A 293 PHE 0.029 0.001 PHE A 109 TRP 0.019 0.001 TRP A 322 HIS 0.010 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4557) covalent geometry : angle 0.54626 ( 6217) SS BOND : bond 0.00517 ( 1) SS BOND : angle 0.91592 ( 2) hydrogen bonds : bond 0.03940 ( 247) hydrogen bonds : angle 4.01111 ( 723) *********************** 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 130 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.139 Fit side-chains REVERT: A 129 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.6757 (m-10) REVERT: A 150 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8141 (t80) REVERT: A 251 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7827 (tp) REVERT: A 291 MET cc_start: 0.7302 (mpt) cc_final: 0.7078 (mpt) REVERT: A 327 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8000 (m) REVERT: A 424 GLU cc_start: 0.7700 (tp30) cc_final: 0.7145 (tp30) REVERT: A 433 GLU cc_start: 0.7966 (tp30) cc_final: 0.7323 (tt0) REVERT: A 516 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7668 (mt) REVERT: A 584 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6831 (m-30) outliers start: 39 outliers final: 30 residues processed: 109 average time/residue: 0.0529 time to fit residues: 7.6610 Evaluate side-chains 126 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.103 ------------------------------------------------------------------------------- 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 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 251 LEU 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 327 THR 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 461 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 489 MET 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 Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 0.0870 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.162747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.151591 restraints weight = 6415.935| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.30 r_work: 0.3716 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4558 Z= 0.115 Angle : 0.548 5.459 6219 Z= 0.283 Chirality : 0.040 0.136 684 Planarity : 0.004 0.038 762 Dihedral : 8.188 78.094 631 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 7.71 % Allowed : 25.05 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.38), residues: 548 helix: 1.21 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.96 (0.50), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 119 TYR 0.024 0.001 TYR A 293 PHE 0.029 0.001 PHE A 109 TRP 0.018 0.001 TRP A 322 HIS 0.010 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4557) covalent geometry : angle 0.54745 ( 6217) SS BOND : bond 0.00435 ( 1) SS BOND : angle 0.93022 ( 2) hydrogen bonds : bond 0.03861 ( 247) hydrogen bonds : angle 3.98653 ( 723) *********************** 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 128 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 129 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6751 (m-10) REVERT: A 150 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.8135 (t80) REVERT: A 251 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7770 (tp) REVERT: A 291 MET cc_start: 0.7294 (mpt) cc_final: 0.7067 (mpt) REVERT: A 327 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.7974 (m) REVERT: A 424 GLU cc_start: 0.7696 (tp30) cc_final: 0.7164 (tp30) REVERT: A 433 GLU cc_start: 0.7953 (tp30) cc_final: 0.7305 (tt0) REVERT: A 516 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7640 (mt) REVERT: A 584 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6809 (m-30) outliers start: 36 outliers final: 29 residues processed: 109 average time/residue: 0.0536 time to fit residues: 7.7258 Evaluate side-chains 126 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 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 251 LEU 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 327 THR 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 461 LEU 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 584 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.0270 chunk 26 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.164550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.153508 restraints weight = 6329.036| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.28 r_work: 0.3716 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4558 Z= 0.116 Angle : 0.549 5.414 6219 Z= 0.283 Chirality : 0.040 0.135 684 Planarity : 0.004 0.056 762 Dihedral : 8.171 78.387 631 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 8.35 % Allowed : 24.84 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.38), residues: 548 helix: 1.21 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.14 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 119 TYR 0.024 0.001 TYR A 293 PHE 0.031 0.001 PHE A 109 TRP 0.019 0.001 TRP A 322 HIS 0.002 0.000 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4557) covalent geometry : angle 0.54933 ( 6217) SS BOND : bond 0.00452 ( 1) SS BOND : angle 0.87423 ( 2) hydrogen bonds : bond 0.03832 ( 247) hydrogen bonds : angle 3.96427 ( 723) ********************** 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 131 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 129 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6747 (m-10) REVERT: A 150 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.8100 (t80) REVERT: A 251 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7761 (tp) REVERT: A 291 MET cc_start: 0.7282 (mpt) cc_final: 0.7051 (mpt) REVERT: A 327 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.7947 (m) REVERT: A 424 GLU cc_start: 0.7694 (tp30) cc_final: 0.7164 (tp30) REVERT: A 433 GLU cc_start: 0.7930 (tp30) cc_final: 0.7272 (tt0) REVERT: A 516 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7623 (mt) outliers start: 39 outliers final: 31 residues processed: 112 average time/residue: 0.0545 time to fit residues: 8.0496 Evaluate side-chains 125 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 104 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 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 251 LEU 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 327 THR 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 461 LEU 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 584 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.164080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.152728 restraints weight = 6420.555| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.37 r_work: 0.3728 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4558 Z= 0.118 Angle : 0.555 5.403 6219 Z= 0.286 Chirality : 0.041 0.133 684 Planarity : 0.004 0.036 762 Dihedral : 8.160 78.606 631 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 7.92 % Allowed : 24.84 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.38), residues: 548 helix: 1.21 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -2.15 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.023 0.001 TYR A 293 PHE 0.031 0.001 PHE A 109 TRP 0.028 0.002 TRP A 600 HIS 0.002 0.000 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4557) covalent geometry : angle 0.55471 ( 6217) SS BOND : bond 0.00469 ( 1) SS BOND : angle 0.88006 ( 2) hydrogen bonds : bond 0.03840 ( 247) hydrogen bonds : angle 3.98368 ( 723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1042.55 seconds wall clock time: 18 minutes 30.82 seconds (1110.82 seconds total)