Starting phenix.real_space_refine on Wed Sep 17 05:06:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3j_61117/09_2025/9j3j_61117.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3j_61117/09_2025/9j3j_61117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j3j_61117/09_2025/9j3j_61117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3j_61117/09_2025/9j3j_61117.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j3j_61117/09_2025/9j3j_61117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3j_61117/09_2025/9j3j_61117.map" } resolution = 2.83 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= 0.000 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 3152 2.51 5 N 751 2.21 5 O 847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4779 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3814 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 25, 'TRANS': 464} Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Time building chain proxies: 1.16, per 1000 atoms: 0.24 Number of scatterers: 4779 At special positions: 0 Unit cell: (79.05, 82.77, 102.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 847 8.00 N 751 7.00 C 3152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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: 0.39 Conformation dependent library (CDL) restraints added in 187.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 72.2% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 110 through 142 Proline residue: A 118 - end of helix removed outlier: 4.252A pdb=" N ASP A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 158 removed outlier: 3.755A pdb=" N PHE A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 removed outlier: 3.528A pdb=" N LYS A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 201 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.526A pdb=" N ILE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.566A pdb=" N ILE A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 266 through 274 Processing helix chain 'A' and resid 274 through 302 removed outlier: 4.753A pdb=" N GLY A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 338 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.115A pdb=" N LYS A 348 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 365 through 397 Processing helix chain 'A' and resid 399 through 432 removed outlier: 4.371A pdb=" N SER A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 458 removed outlier: 3.541A pdb=" N ALA A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 458 through 468 removed outlier: 3.846A pdb=" N PHE A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Proline residue: A 464 - end of helix removed outlier: 3.567A pdb=" N LYS A 468 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 491 Processing helix chain 'A' and resid 495 through 503 removed outlier: 3.820A pdb=" N CYS A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 522 through 543 Processing helix chain 'A' and resid 548 through 590 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.700A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.692A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 361 hydrogen bonds defined for protein. 1047 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: 0.82 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 738 1.29 - 1.42: 1310 1.42 - 1.55: 2805 1.55 - 1.68: 0 1.68 - 1.81: 50 Bond restraints: 4903 Sorted by residual: bond pdb=" C PHE A 542 " pdb=" O PHE A 542 " ideal model delta sigma weight residual 1.233 1.161 0.072 1.43e-02 4.89e+03 2.52e+01 bond pdb=" N TYR B 54 " pdb=" CA TYR B 54 " ideal model delta sigma weight residual 1.456 1.395 0.060 1.33e-02 5.65e+03 2.06e+01 bond pdb=" C TYR B 54 " pdb=" O TYR B 54 " ideal model delta sigma weight residual 1.236 1.179 0.056 1.32e-02 5.74e+03 1.82e+01 bond pdb=" C PHE A 542 " pdb=" N GLY A 543 " ideal model delta sigma weight residual 1.331 1.273 0.058 1.46e-02 4.69e+03 1.57e+01 bond pdb=" CA PHE A 542 " pdb=" CB PHE A 542 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.34e-02 5.57e+03 1.54e+01 ... (remaining 4898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 6529 2.32 - 4.65: 101 4.65 - 6.97: 26 6.97 - 9.29: 1 9.29 - 11.62: 1 Bond angle restraints: 6658 Sorted by residual: angle pdb=" N PHE A 542 " pdb=" CA PHE A 542 " pdb=" C PHE A 542 " ideal model delta sigma weight residual 111.87 118.59 -6.72 1.41e+00 5.03e-01 2.27e+01 angle pdb=" C THR A 342 " pdb=" N ARG A 343 " pdb=" CA ARG A 343 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 angle pdb=" CB MET A 407 " pdb=" CG MET A 407 " pdb=" SD MET A 407 " ideal model delta sigma weight residual 112.70 101.08 11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" N PHE A 542 " pdb=" CA PHE A 542 " pdb=" CB PHE A 542 " ideal model delta sigma weight residual 111.39 105.75 5.64 1.56e+00 4.11e-01 1.31e+01 angle pdb=" N TYR B 54 " pdb=" CA TYR B 54 " pdb=" CB TYR B 54 " ideal model delta sigma weight residual 110.46 104.86 5.60 1.57e+00 4.06e-01 1.27e+01 ... (remaining 6653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 2621 16.59 - 33.18: 204 33.18 - 49.77: 38 49.77 - 66.36: 9 66.36 - 82.95: 2 Dihedral angle restraints: 2874 sinusoidal: 1105 harmonic: 1769 Sorted by residual: dihedral pdb=" CA THR A 342 " pdb=" C THR A 342 " pdb=" N ARG A 343 " pdb=" CA ARG A 343 " ideal model delta harmonic sigma weight residual 180.00 154.69 25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ALA A 215 " pdb=" C ALA A 215 " pdb=" N ASP A 216 " pdb=" CA ASP A 216 " ideal model delta harmonic sigma weight residual 180.00 156.14 23.86 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA MET A 407 " pdb=" C MET A 407 " pdb=" N GLY A 408 " pdb=" CA GLY A 408 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 2871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 493 0.036 - 0.072: 187 0.072 - 0.109: 59 0.109 - 0.145: 10 0.145 - 0.181: 6 Chirality restraints: 755 Sorted by residual: chirality pdb=" CB ILE A 152 " pdb=" CA ILE A 152 " pdb=" CG1 ILE A 152 " pdb=" CG2 ILE A 152 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CG LEU A 340 " pdb=" CB LEU A 340 " pdb=" CD1 LEU A 340 " pdb=" CD2 LEU A 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB ILE A 534 " pdb=" CA ILE A 534 " pdb=" CG1 ILE A 534 " pdb=" CG2 ILE A 534 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 752 not shown) Planarity restraints: 817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 551 " 0.015 2.00e-02 2.50e+03 1.80e-02 6.48e+00 pdb=" CG TYR A 551 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 551 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 551 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 551 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 551 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 551 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 551 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 541 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C SER A 541 " -0.036 2.00e-02 2.50e+03 pdb=" O SER A 541 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 542 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 248 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C TRP A 248 " 0.033 2.00e-02 2.50e+03 pdb=" O TRP A 248 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 249 " -0.011 2.00e-02 2.50e+03 ... (remaining 814 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 701 2.76 - 3.29: 4881 3.29 - 3.83: 8409 3.83 - 4.36: 9806 4.36 - 4.90: 17002 Nonbonded interactions: 40799 Sorted by model distance: nonbonded pdb=" OE1 GLU A 501 " pdb=" NZ LYS A 516 " model vdw 2.222 3.120 nonbonded pdb=" OE2 GLU A 571 " pdb=" ND2 ASN A 575 " model vdw 2.368 3.120 nonbonded pdb=" O LYS A 314 " pdb=" OG SER A 318 " model vdw 2.368 3.040 nonbonded pdb=" NZ LYS A 115 " pdb=" O ILE A 264 " model vdw 2.387 3.120 nonbonded pdb=" O THR A 388 " pdb=" OG SER A 391 " model vdw 2.424 3.040 ... (remaining 40794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.270 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:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4904 Z= 0.241 Angle : 0.732 11.616 6660 Z= 0.393 Chirality : 0.044 0.181 755 Planarity : 0.005 0.045 817 Dihedral : 12.621 82.947 1743 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.18 % 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 (0.33), residues: 608 helix: 0.44 (0.25), residues: 406 sheet: -1.32 (0.66), residues: 46 loop : -1.46 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 66 TYR 0.044 0.002 TYR A 551 PHE 0.030 0.002 PHE A 123 TRP 0.018 0.002 TRP B 110 HIS 0.001 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 4903) covalent geometry : angle 0.73243 ( 6658) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.73250 ( 2) hydrogen bonds : bond 0.12415 ( 355) hydrogen bonds : angle 6.22350 ( 1047) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.131 Fit side-chains REVERT: A 290 ARG cc_start: 0.8819 (mmm160) cc_final: 0.8492 (mmm160) REVERT: A 314 LYS cc_start: 0.8344 (mttt) cc_final: 0.7959 (ttmm) REVERT: A 357 GLU cc_start: 0.7760 (tt0) cc_final: 0.7480 (tt0) REVERT: A 361 PHE cc_start: 0.7408 (t80) cc_final: 0.7060 (t80) REVERT: A 544 SER cc_start: 0.8373 (t) cc_final: 0.8131 (p) REVERT: B 81 GLN cc_start: 0.8571 (tp40) cc_final: 0.8358 (tp-100) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.4639 time to fit residues: 56.7900 Evaluate side-chains 111 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN B 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.173866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.147431 restraints weight = 5772.452| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.89 r_work: 0.3582 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4904 Z= 0.160 Angle : 0.586 6.516 6660 Z= 0.302 Chirality : 0.041 0.125 755 Planarity : 0.005 0.041 817 Dihedral : 4.783 22.121 656 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.75 % Allowed : 10.33 % Favored : 87.91 % 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: 0.66 (0.34), residues: 608 helix: 1.14 (0.25), residues: 413 sheet: -1.05 (0.66), residues: 46 loop : -0.88 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 343 TYR 0.010 0.001 TYR A 194 PHE 0.022 0.002 PHE A 123 TRP 0.009 0.001 TRP A 258 HIS 0.001 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 4903) covalent geometry : angle 0.58637 ( 6658) SS BOND : bond 0.00172 ( 1) SS BOND : angle 0.76748 ( 2) hydrogen bonds : bond 0.05158 ( 355) hydrogen bonds : angle 4.93687 ( 1047) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.179 Fit side-chains REVERT: A 140 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8663 (tt) REVERT: A 290 ARG cc_start: 0.8887 (mmm160) cc_final: 0.8502 (mmm160) REVERT: A 298 LEU cc_start: 0.8721 (tp) cc_final: 0.8443 (tt) REVERT: A 314 LYS cc_start: 0.8481 (mttt) cc_final: 0.8088 (ttmm) REVERT: A 361 PHE cc_start: 0.7590 (t80) cc_final: 0.7362 (t80) REVERT: A 501 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8181 (mm-30) REVERT: B 46 GLU cc_start: 0.8575 (pt0) cc_final: 0.8314 (pt0) outliers start: 9 outliers final: 4 residues processed: 128 average time/residue: 0.4504 time to fit residues: 60.3703 Evaluate side-chains 124 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 7 optimal weight: 0.0270 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN A 301 ASN A 524 ASN B 81 GLN B 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.175165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148592 restraints weight = 5829.682| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.94 r_work: 0.3592 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4904 Z= 0.150 Angle : 0.553 5.893 6660 Z= 0.285 Chirality : 0.040 0.119 755 Planarity : 0.004 0.040 817 Dihedral : 4.576 20.309 656 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.53 % Allowed : 12.48 % Favored : 84.99 % 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: 1.25 (0.34), residues: 608 helix: 1.64 (0.26), residues: 411 sheet: -0.82 (0.65), residues: 46 loop : -0.80 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 343 TYR 0.010 0.001 TYR B 54 PHE 0.016 0.002 PHE A 452 TRP 0.007 0.001 TRP A 258 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4903) covalent geometry : angle 0.55274 ( 6658) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.50760 ( 2) hydrogen bonds : bond 0.04799 ( 355) hydrogen bonds : angle 4.75746 ( 1047) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.154 Fit side-chains REVERT: A 140 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8680 (tt) REVERT: A 290 ARG cc_start: 0.8886 (mmm160) cc_final: 0.8493 (mmm160) REVERT: A 298 LEU cc_start: 0.8751 (tp) cc_final: 0.8469 (tt) REVERT: A 300 LYS cc_start: 0.8494 (mppt) cc_final: 0.8215 (mppt) REVERT: A 309 TRP cc_start: 0.8449 (t-100) cc_final: 0.8143 (t-100) REVERT: A 361 PHE cc_start: 0.7699 (t80) cc_final: 0.7441 (t80) REVERT: A 386 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7896 (tp30) REVERT: B 19 ARG cc_start: 0.8506 (ttt180) cc_final: 0.8264 (ttt-90) REVERT: B 46 GLU cc_start: 0.8627 (pt0) cc_final: 0.8369 (pt0) outliers start: 13 outliers final: 6 residues processed: 122 average time/residue: 0.4267 time to fit residues: 54.6626 Evaluate side-chains 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 53 optimal weight: 0.0000 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 81 GLN B 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.173585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.147112 restraints weight = 5766.997| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.90 r_work: 0.3590 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4904 Z= 0.156 Angle : 0.561 7.698 6660 Z= 0.284 Chirality : 0.040 0.121 755 Planarity : 0.004 0.039 817 Dihedral : 4.529 20.140 656 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.34 % Allowed : 15.98 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.38 (0.34), residues: 608 helix: 1.69 (0.26), residues: 412 sheet: -0.52 (0.68), residues: 46 loop : -0.70 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 299 TYR 0.011 0.001 TYR A 551 PHE 0.016 0.002 PHE A 542 TRP 0.005 0.001 TRP A 258 HIS 0.001 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 4903) covalent geometry : angle 0.56116 ( 6658) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.55352 ( 2) hydrogen bonds : bond 0.04757 ( 355) hydrogen bonds : angle 4.70396 ( 1047) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.136 Fit side-chains REVERT: A 140 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8698 (tt) REVERT: A 207 ASN cc_start: 0.8187 (m-40) cc_final: 0.7767 (p0) REVERT: A 290 ARG cc_start: 0.8853 (mmm160) cc_final: 0.8432 (mmm160) REVERT: A 298 LEU cc_start: 0.8710 (tp) cc_final: 0.8440 (tt) REVERT: A 300 LYS cc_start: 0.8464 (mppt) cc_final: 0.8220 (mppt) REVERT: A 361 PHE cc_start: 0.7674 (t80) cc_final: 0.7401 (t80) REVERT: A 386 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7860 (tp30) REVERT: B 19 ARG cc_start: 0.8516 (ttt180) cc_final: 0.8302 (ttt-90) REVERT: B 46 GLU cc_start: 0.8597 (pt0) cc_final: 0.8345 (pt0) outliers start: 12 outliers final: 7 residues processed: 123 average time/residue: 0.4094 time to fit residues: 52.9015 Evaluate side-chains 123 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 81 GLN B 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.176789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.149437 restraints weight = 5916.692| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.89 r_work: 0.3565 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 4904 Z= 0.193 Angle : 0.600 6.250 6660 Z= 0.300 Chirality : 0.043 0.305 755 Planarity : 0.005 0.039 817 Dihedral : 4.583 20.003 656 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.92 % Allowed : 16.96 % Favored : 80.12 % 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: 1.32 (0.34), residues: 608 helix: 1.63 (0.25), residues: 413 sheet: -0.52 (0.69), residues: 46 loop : -0.68 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 343 TYR 0.013 0.001 TYR B 107 PHE 0.017 0.002 PHE A 542 TRP 0.005 0.001 TRP A 258 HIS 0.001 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 4903) covalent geometry : angle 0.59981 ( 6658) SS BOND : bond 0.00319 ( 1) SS BOND : angle 0.38807 ( 2) hydrogen bonds : bond 0.04999 ( 355) hydrogen bonds : angle 4.74776 ( 1047) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.183 Fit side-chains REVERT: A 140 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8792 (tt) REVERT: A 207 ASN cc_start: 0.8192 (m-40) cc_final: 0.7849 (p0) REVERT: A 290 ARG cc_start: 0.8862 (mmm160) cc_final: 0.8453 (mmm160) REVERT: A 361 PHE cc_start: 0.7653 (t80) cc_final: 0.7381 (t80) REVERT: A 386 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7932 (tp30) REVERT: A 407 MET cc_start: 0.8958 (mmp) cc_final: 0.8617 (mmt) REVERT: A 423 LEU cc_start: 0.8624 (mm) cc_final: 0.8323 (mt) REVERT: B 19 ARG cc_start: 0.8532 (ttt180) cc_final: 0.8310 (ttt-90) REVERT: B 46 GLU cc_start: 0.8606 (pt0) cc_final: 0.8333 (pt0) outliers start: 15 outliers final: 10 residues processed: 119 average time/residue: 0.4308 time to fit residues: 53.8029 Evaluate side-chains 121 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 53 optimal weight: 0.2980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 81 GLN B 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.162693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136790 restraints weight = 5893.263| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.94 r_work: 0.3472 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4904 Z= 0.118 Angle : 0.536 6.496 6660 Z= 0.267 Chirality : 0.039 0.149 755 Planarity : 0.004 0.042 817 Dihedral : 4.386 19.104 656 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.34 % Allowed : 18.32 % Favored : 79.34 % 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: 1.75 (0.35), residues: 608 helix: 1.92 (0.26), residues: 413 sheet: 0.00 (0.73), residues: 46 loop : -0.58 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 578 TYR 0.013 0.001 TYR B 54 PHE 0.021 0.001 PHE A 542 TRP 0.005 0.001 TRP B 47 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4903) covalent geometry : angle 0.53608 ( 6658) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.55640 ( 2) hydrogen bonds : bond 0.04253 ( 355) hydrogen bonds : angle 4.54016 ( 1047) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.199 Fit side-chains REVERT: A 104 LYS cc_start: 0.8249 (mtpt) cc_final: 0.8021 (mtpm) REVERT: A 140 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8494 (tt) REVERT: A 207 ASN cc_start: 0.8005 (m-40) cc_final: 0.7773 (p0) REVERT: A 290 ARG cc_start: 0.8776 (mmm160) cc_final: 0.8407 (mmm160) REVERT: A 298 LEU cc_start: 0.8405 (tp) cc_final: 0.8161 (tt) REVERT: A 361 PHE cc_start: 0.7605 (t80) cc_final: 0.7325 (t80) REVERT: A 386 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7775 (tp30) REVERT: A 431 LYS cc_start: 0.8282 (tttt) cc_final: 0.7959 (tttm) REVERT: B 43 LYS cc_start: 0.8422 (mtpt) cc_final: 0.8150 (mtpp) REVERT: B 46 GLU cc_start: 0.8583 (pt0) cc_final: 0.8334 (pt0) outliers start: 12 outliers final: 5 residues processed: 120 average time/residue: 0.4396 time to fit residues: 55.4749 Evaluate side-chains 112 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.160403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133569 restraints weight = 5805.609| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.97 r_work: 0.3443 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4904 Z= 0.150 Angle : 0.563 7.672 6660 Z= 0.281 Chirality : 0.040 0.128 755 Planarity : 0.004 0.041 817 Dihedral : 4.359 18.587 656 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.95 % Allowed : 19.30 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.73 (0.35), residues: 608 helix: 1.89 (0.26), residues: 413 sheet: -0.02 (0.73), residues: 46 loop : -0.51 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 299 TYR 0.014 0.001 TYR B 54 PHE 0.014 0.001 PHE A 574 TRP 0.005 0.001 TRP A 258 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4903) covalent geometry : angle 0.56295 ( 6658) SS BOND : bond 0.00225 ( 1) SS BOND : angle 0.42660 ( 2) hydrogen bonds : bond 0.04581 ( 355) hydrogen bonds : angle 4.58271 ( 1047) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.185 Fit side-chains REVERT: A 104 LYS cc_start: 0.8232 (mtpt) cc_final: 0.8006 (mtpm) REVERT: A 290 ARG cc_start: 0.8785 (mmm160) cc_final: 0.8415 (mmm160) REVERT: A 298 LEU cc_start: 0.8471 (tp) cc_final: 0.8216 (tt) REVERT: A 343 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.4932 (mmm160) REVERT: A 361 PHE cc_start: 0.7563 (t80) cc_final: 0.7271 (t80) REVERT: A 386 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7772 (tp30) REVERT: A 528 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7146 (mptm) REVERT: B 43 LYS cc_start: 0.8413 (mtpt) cc_final: 0.8132 (mtpp) REVERT: B 46 GLU cc_start: 0.8592 (pt0) cc_final: 0.8325 (pt0) outliers start: 10 outliers final: 6 residues processed: 119 average time/residue: 0.4383 time to fit residues: 54.8303 Evaluate side-chains 115 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.160296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.133331 restraints weight = 5922.695| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.98 r_work: 0.3410 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4904 Z= 0.154 Angle : 0.575 8.347 6660 Z= 0.285 Chirality : 0.041 0.140 755 Planarity : 0.005 0.043 817 Dihedral : 4.377 18.769 656 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.53 % Allowed : 19.10 % Favored : 78.36 % 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: 1.75 (0.34), residues: 608 helix: 1.89 (0.25), residues: 414 sheet: 0.00 (0.72), residues: 46 loop : -0.50 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 299 TYR 0.014 0.001 TYR B 54 PHE 0.023 0.002 PHE A 542 TRP 0.004 0.001 TRP A 258 HIS 0.001 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 4903) covalent geometry : angle 0.57540 ( 6658) SS BOND : bond 0.00235 ( 1) SS BOND : angle 0.49783 ( 2) hydrogen bonds : bond 0.04613 ( 355) hydrogen bonds : angle 4.60098 ( 1047) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.166 Fit side-chains REVERT: A 104 LYS cc_start: 0.8239 (mtpt) cc_final: 0.8024 (mtpm) REVERT: A 290 ARG cc_start: 0.8796 (mmm160) cc_final: 0.8430 (mmm160) REVERT: A 298 LEU cc_start: 0.8530 (tp) cc_final: 0.8277 (tt) REVERT: A 340 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7577 (mt) REVERT: A 343 ARG cc_start: 0.5787 (OUTLIER) cc_final: 0.4905 (mmm160) REVERT: A 361 PHE cc_start: 0.7575 (t80) cc_final: 0.7080 (t80) REVERT: A 386 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7773 (tp30) REVERT: A 423 LEU cc_start: 0.8634 (mm) cc_final: 0.8353 (mt) REVERT: A 431 LYS cc_start: 0.8357 (tttt) cc_final: 0.8042 (tttm) REVERT: B 43 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8130 (mtpp) REVERT: B 46 GLU cc_start: 0.8597 (pt0) cc_final: 0.8324 (pt0) outliers start: 13 outliers final: 8 residues processed: 115 average time/residue: 0.4542 time to fit residues: 54.6848 Evaluate side-chains 118 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.159766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132878 restraints weight = 5852.672| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.98 r_work: 0.3429 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4904 Z= 0.151 Angle : 0.576 9.851 6660 Z= 0.284 Chirality : 0.041 0.146 755 Planarity : 0.005 0.044 817 Dihedral : 4.359 18.772 656 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.34 % Allowed : 19.10 % Favored : 78.56 % 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: 1.80 (0.34), residues: 608 helix: 1.92 (0.25), residues: 414 sheet: 0.04 (0.72), residues: 46 loop : -0.45 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 299 TYR 0.014 0.001 TYR B 54 PHE 0.013 0.001 PHE A 574 TRP 0.005 0.001 TRP A 258 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4903) covalent geometry : angle 0.57625 ( 6658) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.47477 ( 2) hydrogen bonds : bond 0.04594 ( 355) hydrogen bonds : angle 4.60598 ( 1047) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.229 Fit side-chains REVERT: A 104 LYS cc_start: 0.8233 (mtpt) cc_final: 0.8017 (mtpm) REVERT: A 290 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8413 (mmm160) REVERT: A 298 LEU cc_start: 0.8527 (tp) cc_final: 0.8275 (tt) REVERT: A 340 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7558 (mt) REVERT: A 343 ARG cc_start: 0.5851 (OUTLIER) cc_final: 0.4965 (mmm160) REVERT: A 361 PHE cc_start: 0.7566 (t80) cc_final: 0.7060 (t80) REVERT: A 386 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7799 (tp30) REVERT: A 423 LEU cc_start: 0.8602 (mm) cc_final: 0.8286 (mt) REVERT: A 431 LYS cc_start: 0.8370 (tttt) cc_final: 0.8049 (tttm) REVERT: B 43 LYS cc_start: 0.8432 (mtpt) cc_final: 0.8157 (mtpp) REVERT: B 46 GLU cc_start: 0.8592 (pt0) cc_final: 0.8318 (pt0) outliers start: 12 outliers final: 8 residues processed: 115 average time/residue: 0.4673 time to fit residues: 56.2928 Evaluate side-chains 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 81 GLN B 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132479 restraints weight = 5801.218| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.96 r_work: 0.3429 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4904 Z= 0.156 Angle : 0.584 9.757 6660 Z= 0.288 Chirality : 0.041 0.150 755 Planarity : 0.005 0.045 817 Dihedral : 4.373 18.986 656 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.53 % Allowed : 19.69 % Favored : 77.78 % 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: 1.83 (0.34), residues: 608 helix: 1.94 (0.25), residues: 414 sheet: -0.01 (0.72), residues: 46 loop : -0.38 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 299 TYR 0.016 0.001 TYR B 54 PHE 0.025 0.002 PHE A 542 TRP 0.004 0.001 TRP A 258 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 4903) covalent geometry : angle 0.58362 ( 6658) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.46422 ( 2) hydrogen bonds : bond 0.04627 ( 355) hydrogen bonds : angle 4.60459 ( 1047) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.199 Fit side-chains REVERT: A 104 LYS cc_start: 0.8240 (mtpt) cc_final: 0.8029 (mtpm) REVERT: A 168 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7985 (ptm) REVERT: A 290 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8414 (mmm160) REVERT: A 298 LEU cc_start: 0.8522 (tp) cc_final: 0.8270 (tt) REVERT: A 340 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7545 (mt) REVERT: A 343 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.4999 (mmm160) REVERT: A 361 PHE cc_start: 0.7576 (t80) cc_final: 0.7097 (t80) REVERT: A 386 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7801 (tp30) REVERT: A 423 LEU cc_start: 0.8589 (mm) cc_final: 0.8280 (mt) REVERT: A 431 LYS cc_start: 0.8409 (tttt) cc_final: 0.8107 (tttm) REVERT: B 43 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8153 (mtpp) REVERT: B 46 GLU cc_start: 0.8591 (pt0) cc_final: 0.8315 (pt0) outliers start: 13 outliers final: 8 residues processed: 112 average time/residue: 0.4674 time to fit residues: 54.7967 Evaluate side-chains 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 59 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.159399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133185 restraints weight = 5818.260| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.92 r_work: 0.3439 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4904 Z= 0.150 Angle : 0.580 10.453 6660 Z= 0.286 Chirality : 0.041 0.151 755 Planarity : 0.005 0.046 817 Dihedral : 4.353 18.985 656 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.92 % Allowed : 19.69 % Favored : 77.39 % 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: 1.87 (0.35), residues: 608 helix: 1.96 (0.25), residues: 415 sheet: 0.04 (0.72), residues: 46 loop : -0.39 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 299 TYR 0.015 0.001 TYR B 54 PHE 0.024 0.002 PHE A 542 TRP 0.004 0.001 TRP A 389 HIS 0.001 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4903) covalent geometry : angle 0.57958 ( 6658) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.44222 ( 2) hydrogen bonds : bond 0.04569 ( 355) hydrogen bonds : angle 4.58888 ( 1047) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.08 seconds wall clock time: 34 minutes 25.52 seconds (2065.52 seconds total)