Starting phenix.real_space_refine on Wed Jul 1 22:12:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wb5_32395/07_2026/7wb5_32395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wb5_32395/07_2026/7wb5_32395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wb5_32395/07_2026/7wb5_32395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wb5_32395/07_2026/7wb5_32395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wb5_32395/07_2026/7wb5_32395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wb5_32395/07_2026/7wb5_32395.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wb5_32395/07_2026/7wb5_32395.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wb5_32395/07_2026/7wb5_32395.cif" } resolution = 3.7 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= 0.022 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 15 5.16 5 C 2077 2.51 5 N 533 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3256 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.28, per 1000 atoms: 0.39 Number of scatterers: 3256 At special positions: 0 Unit cell: (72.36, 88.56, 72.36, 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 15 16.00 O 631 8.00 N 533 7.00 C 2077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.02 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 145.4 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 12 sheets defined 4.4% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 364 through 370 removed outlier: 4.598A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.682A pdb=" N LYS H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.906A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.533A pdb=" N TRP H 50 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.846A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU L 73 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.595A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.572A pdb=" N GLN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.884A pdb=" N ILE R 434 " --> pdb=" O VAL R 511 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS R 432 " --> pdb=" O LEU R 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'R' and resid 473 through 474 73 hydrogen bonds defined for protein. 171 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: 0.43 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 734 1.33 - 1.45: 857 1.45 - 1.57: 1735 1.57 - 1.69: 1 1.69 - 1.82: 18 Bond restraints: 3345 Sorted by residual: bond pdb=" CA SER R 438 " pdb=" CB SER R 438 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.35e-02 5.49e+03 1.53e+01 bond pdb=" CA SER R 349 " pdb=" CB SER R 349 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.64e-02 3.72e+03 1.43e+01 bond pdb=" N LEU R 452 " pdb=" CA LEU R 452 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.22e-02 6.72e+03 1.23e+01 bond pdb=" N VAL R 433 " pdb=" CA VAL R 433 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N LYS R 378 " pdb=" CA LYS R 378 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 ... (remaining 3340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 4160 2.59 - 5.17: 364 5.17 - 7.76: 19 7.76 - 10.34: 3 10.34 - 12.93: 2 Bond angle restraints: 4548 Sorted by residual: angle pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" CD PRO L 80 " ideal model delta sigma weight residual 112.00 99.07 12.93 1.40e+00 5.10e-01 8.52e+01 angle pdb=" CA TRP R 436 " pdb=" CB TRP R 436 " pdb=" CG TRP R 436 " ideal model delta sigma weight residual 113.60 123.83 -10.23 1.90e+00 2.77e-01 2.90e+01 angle pdb=" CA PHE R 400 " pdb=" CB PHE R 400 " pdb=" CG PHE R 400 " ideal model delta sigma weight residual 113.80 118.30 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N PRO L 80 " pdb=" CD PRO L 80 " pdb=" CG PRO L 80 " ideal model delta sigma weight residual 103.20 96.90 6.30 1.50e+00 4.44e-01 1.77e+01 angle pdb=" N LEU R 387 " pdb=" CA LEU R 387 " pdb=" C LEU R 387 " ideal model delta sigma weight residual 114.75 109.56 5.19 1.26e+00 6.30e-01 1.69e+01 ... (remaining 4543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 1605 16.17 - 32.35: 206 32.35 - 48.52: 70 48.52 - 64.70: 33 64.70 - 80.87: 6 Dihedral angle restraints: 1920 sinusoidal: 740 harmonic: 1180 Sorted by residual: dihedral pdb=" CA VAL L 29 " pdb=" C VAL L 29 " pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta harmonic sigma weight residual 180.00 -139.90 -40.10 0 5.00e+00 4.00e-02 6.43e+01 dihedral pdb=" CA PHE H 106 " pdb=" C PHE H 106 " pdb=" N ASP H 107 " pdb=" CA ASP H 107 " ideal model delta harmonic sigma weight residual 180.00 -146.68 -33.32 0 5.00e+00 4.00e-02 4.44e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 136.78 -43.78 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 1917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 417 0.119 - 0.238: 63 0.238 - 0.356: 5 0.356 - 0.475: 0 0.475 - 0.593: 2 Chirality restraints: 487 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.89e+01 chirality pdb=" C1 BMA A 3 " pdb=" O4 NAG A 2 " pdb=" C2 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.29e+01 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN R 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.81e+00 ... (remaining 484 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.304 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" C7 NAG A 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.009 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.453 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.292 2.00e-02 2.50e+03 2.51e-01 7.91e+02 pdb=" C7 NAG A 1 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.443 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.111 5.00e-02 4.00e+02 1.57e-01 3.92e+01 pdb=" N PRO L 80 " 0.270 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.076 5.00e-02 4.00e+02 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 281 2.73 - 3.27: 3255 3.27 - 3.82: 5356 3.82 - 4.36: 6706 4.36 - 4.90: 11080 Nonbonded interactions: 26678 Sorted by model distance: nonbonded pdb=" O ILE L 21 " pdb=" OG1 THR L 72 " model vdw 2.188 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 113 " model vdw 2.319 3.040 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLN L 27 " model vdw 2.405 3.040 nonbonded pdb=" O VAL H 76 " pdb=" OG SER H 77 " model vdw 2.421 3.040 ... (remaining 26673 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 group one per residue 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: 4.230 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.580 Find NCS groups from input model: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.011 0.132 3353 Z= 0.659 Angle : 1.420 12.925 4567 Z= 0.928 Chirality : 0.090 0.593 487 Planarity : 0.018 0.262 581 Dihedral : 18.471 80.870 1159 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 2.24 % Allowed : 18.16 % Favored : 79.60 % Rotamer: Outliers : 14.00 % Allowed : 7.43 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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 are not related in a simple way. whole: -4.90 (0.36), residues: 402 helix: -4.22 (0.64), residues: 21 sheet: -3.58 (0.39), residues: 121 loop : -3.14 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.024 0.003 TYR L 49 PHE 0.023 0.003 PHE R 400 TRP 0.092 0.006 TRP H 109 HIS 0.001 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.01062 / 0.66 ( 3345) covalent geometry : angle 1.40708 / 0.93 ( 4548) SS BOND : bond 0.00729 / 0.40 ( 5) SS BOND : angle 2.86471 / 2.15 ( 10) hydrogen bonds : bond 0.24913 / 17.04 ( 63) hydrogen bonds : angle 11.58444 / 7.32 ( 171) link_BETA1-4 : bond 0.00673 / 0.33 ( 2) link_BETA1-4 : angle 4.14677 / 2.71 ( 6) link_NAG-ASN : bond 0.02467 / 1.30 ( 1) link_NAG-ASN : angle 2.58754 / 1.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: H 83 ILE cc_start: 0.9173 (tt) cc_final: 0.8932 (tt) REVERT: L 74 THR cc_start: 0.7091 (m) cc_final: 0.6571 (m) REVERT: L 79 GLN cc_start: 0.8296 (mp10) cc_final: 0.7806 (mp10) REVERT: R 369 TYR cc_start: 0.7979 (t80) cc_final: 0.7755 (t80) REVERT: R 387 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8498 (tt) REVERT: R 454 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7653 (mtp-110) REVERT: R 493 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7989 (tm-30) outliers start: 49 outliers final: 12 residues processed: 150 average time/residue: 0.0759 time to fit residues: 13.4935 Evaluate side-chains 120 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 422 ASN Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 454 ARG Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 493 GLN Chi-restraints excluded: chain R residue 516 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 82 GLN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113477 restraints weight = 5150.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116282 restraints weight = 3288.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118073 restraints weight = 2440.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119335 restraints weight = 2010.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120105 restraints weight = 1758.744| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3353 Z= 0.200 Angle : 0.847 9.648 4567 Z= 0.431 Chirality : 0.050 0.211 487 Planarity : 0.007 0.085 581 Dihedral : 11.069 58.725 483 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.44 % Favored : 88.06 % Rotamer: Outliers : 7.43 % Allowed : 18.29 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -4.52 (0.36), residues: 402 helix: -3.46 (0.77), residues: 21 sheet: -3.18 (0.43), residues: 113 loop : -3.03 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 18 TYR 0.019 0.002 TYR L 49 PHE 0.026 0.002 PHE R 515 TRP 0.051 0.004 TRP H 109 HIS 0.002 0.002 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 3345) covalent geometry : angle 0.83802 / 0.43 ( 4548) SS BOND : bond 0.00500 / 0.36 ( 5) SS BOND : angle 1.54404 / 0.83 ( 10) hydrogen bonds : bond 0.04718 / 3.30 ( 63) hydrogen bonds : angle 7.28299 / 4.89 ( 171) link_BETA1-4 : bond 0.00841 / 0.44 ( 2) link_BETA1-4 : angle 3.05348 / 2.05 ( 6) link_NAG-ASN : bond 0.00102 / 0.05 ( 1) link_NAG-ASN : angle 1.22622 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8435 (m-80) cc_final: 0.8206 (m-80) REVERT: H 104 TRP cc_start: 0.8767 (m100) cc_final: 0.8338 (m100) REVERT: L 79 GLN cc_start: 0.8350 (mp10) cc_final: 0.7658 (mp10) REVERT: L 100 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7134 (tm-30) REVERT: R 387 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8400 (tt) REVERT: R 408 ARG cc_start: 0.8830 (mtm110) cc_final: 0.8131 (ptm160) REVERT: R 414 GLN cc_start: 0.7946 (tp40) cc_final: 0.7309 (tp-100) REVERT: R 493 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: R 516 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7495 (pp20) outliers start: 26 outliers final: 19 residues processed: 120 average time/residue: 0.0799 time to fit residues: 11.3043 Evaluate side-chains 120 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 422 ASN Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 493 GLN Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 516 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.0060 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.0170 chunk 37 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 82 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.142432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118518 restraints weight = 5065.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121289 restraints weight = 3208.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123104 restraints weight = 2375.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124421 restraints weight = 1942.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125051 restraints weight = 1688.717| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3353 Z= 0.152 Angle : 0.734 8.092 4567 Z= 0.370 Chirality : 0.048 0.211 487 Planarity : 0.006 0.080 581 Dihedral : 9.698 54.736 477 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.45 % Favored : 89.05 % Rotamer: Outliers : 6.57 % Allowed : 20.00 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -4.03 (0.37), residues: 402 helix: -3.65 (0.73), residues: 21 sheet: -2.35 (0.47), residues: 107 loop : -2.91 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 408 TYR 0.019 0.001 TYR H 105 PHE 0.024 0.002 PHE R 515 TRP 0.037 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 3345) covalent geometry : angle 0.72644 / 0.37 ( 4548) SS BOND : bond 0.00282 / 0.15 ( 5) SS BOND : angle 1.12367 / 0.60 ( 10) hydrogen bonds : bond 0.03742 / 2.64 ( 63) hydrogen bonds : angle 6.66201 / 4.51 ( 171) link_BETA1-4 : bond 0.01005 / 0.53 ( 2) link_BETA1-4 : angle 2.72349 / 1.76 ( 6) link_NAG-ASN : bond 0.00336 / 0.18 ( 1) link_NAG-ASN : angle 1.42563 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8315 (m-80) cc_final: 0.8073 (m-10) REVERT: H 90 ASP cc_start: 0.7901 (m-30) cc_final: 0.7498 (m-30) REVERT: L 79 GLN cc_start: 0.8442 (mp10) cc_final: 0.8072 (mp10) REVERT: L 100 GLN cc_start: 0.7454 (tm-30) cc_final: 0.7121 (tm-30) REVERT: R 387 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8362 (tt) REVERT: R 462 LYS cc_start: 0.8463 (pptt) cc_final: 0.8070 (ptmm) REVERT: R 466 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7260 (ptm-80) REVERT: R 493 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7492 (tm-30) outliers start: 23 outliers final: 18 residues processed: 123 average time/residue: 0.0706 time to fit residues: 10.3756 Evaluate side-chains 116 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111291 restraints weight = 5150.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.114124 restraints weight = 4314.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.114983 restraints weight = 2900.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115160 restraints weight = 2454.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115568 restraints weight = 2335.874| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 3353 Z= 0.266 Angle : 0.794 7.449 4567 Z= 0.409 Chirality : 0.049 0.202 487 Planarity : 0.006 0.076 581 Dihedral : 8.683 59.726 463 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.69 % Favored : 87.81 % Rotamer: Outliers : 7.71 % Allowed : 22.00 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -4.24 (0.37), residues: 402 helix: -3.90 (0.76), residues: 21 sheet: -2.94 (0.42), residues: 127 loop : -2.75 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 18 TYR 0.028 0.002 TYR L 49 PHE 0.020 0.002 PHE R 515 TRP 0.059 0.004 TRP H 109 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.27 ( 3345) covalent geometry : angle 0.78561 / 0.41 ( 4548) SS BOND : bond 0.00220 / 0.11 ( 5) SS BOND : angle 1.31996 / 0.77 ( 10) hydrogen bonds : bond 0.04195 / 2.85 ( 63) hydrogen bonds : angle 6.24065 / 4.13 ( 171) link_BETA1-4 : bond 0.00562 / 0.30 ( 2) link_BETA1-4 : angle 3.00321 / 2.13 ( 6) link_NAG-ASN : bond 0.00813 / 0.43 ( 1) link_NAG-ASN : angle 0.99699 / 0.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.128 Fit side-chains REVERT: H 34 MET cc_start: 0.9023 (tpp) cc_final: 0.8763 (tpp) REVERT: H 60 TYR cc_start: 0.8580 (m-80) cc_final: 0.8205 (m-10) REVERT: L 62 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7394 (p90) REVERT: L 79 GLN cc_start: 0.8492 (mp10) cc_final: 0.8067 (mp10) REVERT: L 100 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7160 (tm-30) REVERT: R 387 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8423 (tt) REVERT: R 408 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8371 (ptm160) REVERT: R 493 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7486 (tm-30) REVERT: R 508 TYR cc_start: 0.6651 (m-80) cc_final: 0.6099 (m-80) outliers start: 27 outliers final: 20 residues processed: 112 average time/residue: 0.0770 time to fit residues: 10.2258 Evaluate side-chains 108 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 437 ASN R 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.142463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117953 restraints weight = 4908.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121292 restraints weight = 4408.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121594 restraints weight = 2701.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.122803 restraints weight = 2488.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122805 restraints weight = 2203.292| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3353 Z= 0.194 Angle : 0.738 7.440 4567 Z= 0.376 Chirality : 0.047 0.204 487 Planarity : 0.006 0.079 581 Dihedral : 7.915 54.278 462 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.95 % Favored : 89.80 % Rotamer: Outliers : 8.00 % Allowed : 24.00 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -4.09 (0.37), residues: 402 helix: -3.06 (0.99), residues: 19 sheet: -2.78 (0.46), residues: 116 loop : -2.80 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 18 TYR 0.020 0.002 TYR L 49 PHE 0.015 0.002 PHE R 392 TRP 0.036 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 ( 3345) covalent geometry : angle 0.72895 / 0.37 ( 4548) SS BOND : bond 0.00296 / 0.15 ( 5) SS BOND : angle 1.21320 / 0.68 ( 10) hydrogen bonds : bond 0.03531 / 2.44 ( 63) hydrogen bonds : angle 5.92526 / 4.00 ( 171) link_BETA1-4 : bond 0.00916 / 0.48 ( 2) link_BETA1-4 : angle 2.92924 / 1.95 ( 6) link_NAG-ASN : bond 0.00488 / 0.26 ( 1) link_NAG-ASN : angle 0.97971 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7206 (mp10) cc_final: 0.6801 (mp10) REVERT: H 60 TYR cc_start: 0.8443 (m-80) cc_final: 0.8163 (m-10) REVERT: L 62 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7402 (p90) REVERT: L 79 GLN cc_start: 0.8471 (mp10) cc_final: 0.8060 (mp10) REVERT: L 100 GLN cc_start: 0.7462 (tm-30) cc_final: 0.7145 (tm-30) REVERT: R 387 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8426 (tt) REVERT: R 409 GLN cc_start: 0.8449 (mt0) cc_final: 0.8210 (mt0) REVERT: R 453 TYR cc_start: 0.8728 (p90) cc_final: 0.8298 (p90) REVERT: R 493 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7634 (tm-30) REVERT: R 508 TYR cc_start: 0.6432 (m-80) cc_final: 0.6147 (m-80) outliers start: 28 outliers final: 23 residues processed: 113 average time/residue: 0.0687 time to fit residues: 9.3183 Evaluate side-chains 113 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117809 restraints weight = 5047.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120587 restraints weight = 3349.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122428 restraints weight = 2564.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123268 restraints weight = 2139.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124353 restraints weight = 1934.354| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3353 Z= 0.182 Angle : 0.728 7.316 4567 Z= 0.369 Chirality : 0.047 0.191 487 Planarity : 0.006 0.078 581 Dihedral : 7.618 54.731 461 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.70 % Favored : 90.05 % Rotamer: Outliers : 9.14 % Allowed : 23.71 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -4.01 (0.38), residues: 402 helix: -2.59 (1.19), residues: 18 sheet: -2.83 (0.43), residues: 122 loop : -2.70 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 403 TYR 0.029 0.002 TYR R 380 PHE 0.012 0.002 PHE R 515 TRP 0.053 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 3345) covalent geometry : angle 0.71895 / 0.37 ( 4548) SS BOND : bond 0.00098 / 0.05 ( 5) SS BOND : angle 1.13206 / 0.66 ( 10) hydrogen bonds : bond 0.03399 / 2.34 ( 63) hydrogen bonds : angle 5.78575 / 3.92 ( 171) link_BETA1-4 : bond 0.00912 / 0.48 ( 2) link_BETA1-4 : angle 2.95252 / 1.98 ( 6) link_NAG-ASN : bond 0.00375 / 0.20 ( 1) link_NAG-ASN : angle 0.88180 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7176 (mp10) cc_final: 0.6737 (mp10) REVERT: H 60 TYR cc_start: 0.8416 (m-80) cc_final: 0.8105 (m-10) REVERT: L 62 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7385 (p90) REVERT: L 79 GLN cc_start: 0.8560 (mp10) cc_final: 0.8082 (mp10) REVERT: L 100 GLN cc_start: 0.7446 (tm-30) cc_final: 0.7131 (tm-30) REVERT: R 387 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8428 (tt) REVERT: R 408 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8112 (ptm160) REVERT: R 493 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7473 (tm-30) outliers start: 32 outliers final: 24 residues processed: 114 average time/residue: 0.0733 time to fit residues: 9.9510 Evaluate side-chains 113 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 455 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.147475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123558 restraints weight = 5037.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124734 restraints weight = 4748.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125929 restraints weight = 3753.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.126561 restraints weight = 2971.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.126707 restraints weight = 2721.082| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3353 Z= 0.173 Angle : 0.724 7.277 4567 Z= 0.370 Chirality : 0.047 0.184 487 Planarity : 0.006 0.076 581 Dihedral : 7.505 54.131 460 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.20 % Favored : 90.55 % Rotamer: Outliers : 7.71 % Allowed : 25.14 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -3.97 (0.37), residues: 402 helix: -2.88 (1.03), residues: 19 sheet: -2.85 (0.42), residues: 125 loop : -2.60 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.020 0.002 TYR H 105 PHE 0.011 0.002 PHE R 515 TRP 0.050 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 3345) covalent geometry : angle 0.71555 / 0.37 ( 4548) SS BOND : bond 0.00427 / 0.21 ( 5) SS BOND : angle 1.12717 / 0.67 ( 10) hydrogen bonds : bond 0.03354 / 2.32 ( 63) hydrogen bonds : angle 5.72156 / 3.89 ( 171) link_BETA1-4 : bond 0.00932 / 0.49 ( 2) link_BETA1-4 : angle 2.91122 / 1.92 ( 6) link_NAG-ASN : bond 0.00310 / 0.16 ( 1) link_NAG-ASN : angle 0.82879 / 0.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7218 (mp10) cc_final: 0.6864 (mp10) REVERT: H 60 TYR cc_start: 0.8383 (m-80) cc_final: 0.8079 (m-10) REVERT: L 62 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7461 (p90) REVERT: L 100 GLN cc_start: 0.7400 (tm-30) cc_final: 0.7142 (tm-30) REVERT: R 387 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8387 (tt) REVERT: R 453 TYR cc_start: 0.8639 (p90) cc_final: 0.8297 (p90) REVERT: R 454 ARG cc_start: 0.7625 (mtp85) cc_final: 0.7164 (mtp85) REVERT: R 493 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7428 (tm-30) REVERT: R 508 TYR cc_start: 0.5621 (m-80) cc_final: 0.4912 (m-80) outliers start: 27 outliers final: 22 residues processed: 109 average time/residue: 0.0766 time to fit residues: 9.9519 Evaluate side-chains 113 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.147337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125495 restraints weight = 5069.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125217 restraints weight = 4139.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126007 restraints weight = 3826.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.126305 restraints weight = 3454.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126628 restraints weight = 3172.405| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3353 Z= 0.192 Angle : 0.768 12.111 4567 Z= 0.384 Chirality : 0.047 0.189 487 Planarity : 0.006 0.075 581 Dihedral : 7.445 57.394 458 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.45 % Favored : 89.30 % Rotamer: Outliers : 7.71 % Allowed : 25.14 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -3.87 (0.37), residues: 402 helix: -3.10 (0.90), residues: 18 sheet: -2.79 (0.44), residues: 116 loop : -2.55 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 403 TYR 0.021 0.002 TYR H 105 PHE 0.011 0.002 PHE R 515 TRP 0.048 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 ( 3345) covalent geometry : angle 0.75918 / 0.38 ( 4548) SS BOND : bond 0.00261 / 0.13 ( 5) SS BOND : angle 1.19211 / 0.73 ( 10) hydrogen bonds : bond 0.03359 / 2.30 ( 63) hydrogen bonds : angle 5.87018 / 3.96 ( 171) link_BETA1-4 : bond 0.00954 / 0.50 ( 2) link_BETA1-4 : angle 2.97144 / 1.98 ( 6) link_NAG-ASN : bond 0.00367 / 0.19 ( 1) link_NAG-ASN : angle 0.78896 / 0.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7254 (mp10) cc_final: 0.6818 (mp10) REVERT: H 60 TYR cc_start: 0.8408 (m-80) cc_final: 0.8063 (m-10) REVERT: H 69 VAL cc_start: 0.8236 (t) cc_final: 0.7917 (t) REVERT: H 104 TRP cc_start: 0.8675 (m100) cc_final: 0.8403 (m100) REVERT: L 62 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7459 (p90) REVERT: L 79 GLN cc_start: 0.8599 (mp10) cc_final: 0.8081 (mp10) REVERT: L 100 GLN cc_start: 0.7348 (tm-30) cc_final: 0.7100 (tm-30) REVERT: R 387 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8399 (tt) REVERT: R 408 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8260 (ptm-80) REVERT: R 453 TYR cc_start: 0.8701 (p90) cc_final: 0.8465 (p90) REVERT: R 493 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7342 (tm-30) outliers start: 27 outliers final: 23 residues processed: 109 average time/residue: 0.0773 time to fit residues: 10.0090 Evaluate side-chains 116 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 455 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 37 optimal weight: 0.0270 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.149182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.125740 restraints weight = 5027.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127251 restraints weight = 4383.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128145 restraints weight = 3437.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128538 restraints weight = 3003.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.128869 restraints weight = 2707.933| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3353 Z= 0.165 Angle : 0.759 11.724 4567 Z= 0.381 Chirality : 0.047 0.201 487 Planarity : 0.006 0.075 581 Dihedral : 7.350 59.335 458 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.70 % Favored : 90.05 % Rotamer: Outliers : 8.00 % Allowed : 25.14 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -3.76 (0.37), residues: 402 helix: -3.33 (0.84), residues: 18 sheet: -2.74 (0.46), residues: 109 loop : -2.45 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.021 0.002 TYR H 105 PHE 0.018 0.002 PHE R 400 TRP 0.044 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 3345) covalent geometry : angle 0.75095 / 0.38 ( 4548) SS BOND : bond 0.00161 / 0.08 ( 5) SS BOND : angle 1.16682 / 0.71 ( 10) hydrogen bonds : bond 0.03067 / 2.11 ( 63) hydrogen bonds : angle 5.87207 / 3.97 ( 171) link_BETA1-4 : bond 0.00993 / 0.52 ( 2) link_BETA1-4 : angle 2.91036 / 1.90 ( 6) link_NAG-ASN : bond 0.00220 / 0.12 ( 1) link_NAG-ASN : angle 0.79906 / 0.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 SER cc_start: 0.8797 (p) cc_final: 0.8591 (m) REVERT: H 43 GLN cc_start: 0.7288 (mp10) cc_final: 0.6859 (mp10) REVERT: H 60 TYR cc_start: 0.8359 (m-80) cc_final: 0.8046 (m-10) REVERT: H 104 TRP cc_start: 0.8624 (m100) cc_final: 0.8386 (m100) REVERT: L 62 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7374 (p90) REVERT: L 74 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6907 (p) REVERT: L 79 GLN cc_start: 0.8595 (mp10) cc_final: 0.8060 (mp10) REVERT: L 100 GLN cc_start: 0.7364 (tm-30) cc_final: 0.7157 (tm-30) REVERT: R 387 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8296 (tt) REVERT: R 408 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8120 (ptm-80) REVERT: R 466 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6596 (mtm110) REVERT: R 493 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7329 (tm-30) outliers start: 28 outliers final: 22 residues processed: 111 average time/residue: 0.0718 time to fit residues: 9.5511 Evaluate side-chains 116 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124872 restraints weight = 5044.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124492 restraints weight = 4402.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125118 restraints weight = 4120.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125723 restraints weight = 3626.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126074 restraints weight = 3201.780| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3353 Z= 0.208 Angle : 0.779 11.636 4567 Z= 0.392 Chirality : 0.047 0.201 487 Planarity : 0.006 0.074 581 Dihedral : 7.335 53.248 458 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.45 % Favored : 89.30 % Rotamer: Outliers : 7.71 % Allowed : 25.71 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -3.70 (0.38), residues: 402 helix: -3.81 (0.77), residues: 20 sheet: -2.68 (0.46), residues: 111 loop : -2.35 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 403 TYR 0.023 0.002 TYR H 105 PHE 0.011 0.002 PHE R 515 TRP 0.052 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 ( 3345) covalent geometry : angle 0.77046 / 0.39 ( 4548) SS BOND : bond 0.00178 / 0.09 ( 5) SS BOND : angle 1.30578 / 0.81 ( 10) hydrogen bonds : bond 0.03369 / 2.29 ( 63) hydrogen bonds : angle 5.86760 / 3.96 ( 171) link_BETA1-4 : bond 0.00843 / 0.44 ( 2) link_BETA1-4 : angle 2.98721 / 2.03 ( 6) link_NAG-ASN : bond 0.00495 / 0.26 ( 1) link_NAG-ASN : angle 1.00542 / 0.51 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 SER cc_start: 0.8823 (p) cc_final: 0.8598 (m) REVERT: H 43 GLN cc_start: 0.7223 (mp10) cc_final: 0.6784 (mp10) REVERT: H 60 TYR cc_start: 0.8430 (m-80) cc_final: 0.8149 (m-10) REVERT: H 69 VAL cc_start: 0.8250 (t) cc_final: 0.7926 (t) REVERT: H 104 TRP cc_start: 0.8641 (m100) cc_final: 0.8396 (m100) REVERT: L 62 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7501 (p90) REVERT: L 79 GLN cc_start: 0.8625 (mp10) cc_final: 0.8062 (mp10) REVERT: L 100 GLN cc_start: 0.7455 (tm-30) cc_final: 0.7209 (tm-30) REVERT: R 387 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8413 (tt) REVERT: R 466 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6683 (mtm110) REVERT: R 493 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7633 (tm-30) outliers start: 27 outliers final: 21 residues processed: 111 average time/residue: 0.0659 time to fit residues: 8.7747 Evaluate side-chains 116 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.148421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.126316 restraints weight = 5017.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126639 restraints weight = 3944.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127392 restraints weight = 3627.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.127749 restraints weight = 3115.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.127986 restraints weight = 2903.380| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3353 Z= 0.182 Angle : 0.765 11.476 4567 Z= 0.385 Chirality : 0.047 0.210 487 Planarity : 0.006 0.074 581 Dihedral : 7.193 47.271 458 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.70 % Favored : 90.05 % Rotamer: Outliers : 6.86 % Allowed : 25.71 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -3.69 (0.38), residues: 402 helix: -3.76 (0.78), residues: 20 sheet: -2.63 (0.43), residues: 121 loop : -2.33 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 18 TYR 0.023 0.002 TYR H 105 PHE 0.011 0.002 PHE R 400 TRP 0.050 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 3345) covalent geometry : angle 0.75610 / 0.38 ( 4548) SS BOND : bond 0.00165 / 0.08 ( 5) SS BOND : angle 1.23835 / 0.76 ( 10) hydrogen bonds : bond 0.03281 / 2.25 ( 63) hydrogen bonds : angle 5.84235 / 3.95 ( 171) link_BETA1-4 : bond 0.00936 / 0.49 ( 2) link_BETA1-4 : angle 2.95886 / 1.97 ( 6) link_NAG-ASN : bond 0.00365 / 0.19 ( 1) link_NAG-ASN : angle 0.88264 / 0.45 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 910.83 seconds wall clock time: 16 minutes 23.83 seconds (983.83 seconds total)