Starting phenix.real_space_refine on Wed Sep 17 03:32:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgr_50418/09_2025/9fgr_50418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgr_50418/09_2025/9fgr_50418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fgr_50418/09_2025/9fgr_50418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgr_50418/09_2025/9fgr_50418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fgr_50418/09_2025/9fgr_50418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgr_50418/09_2025/9fgr_50418.map" } resolution = 4.0 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= -0.003 sd= 0.051 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 14 5.16 5 C 2042 2.51 5 N 537 2.21 5 O 616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3209 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1511 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 10, 'TRANS': 179} Chain breaks: 1 Chain: "E" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1683 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.99, per 1000 atoms: 0.31 Number of scatterers: 3209 At special positions: 0 Unit cell: (82.677, 62.23, 81.788, 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 14 16.00 O 616 8.00 N 537 7.00 C 2042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 109.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 7.3% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.099A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.389A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 removed outlier: 3.963A pdb=" N PHE E 217 " --> pdb=" O PRO E 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.015A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.959A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS E 22 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 78 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.649A pdb=" N GLY E 10 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR E 115 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 50 " --> pdb=" O PHE E 58 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E 58 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 137 through 139 removed outlier: 3.514A pdb=" N THR E 138 " --> pdb=" O ARG E 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 187 through 188 removed outlier: 5.792A pdb=" N LEU E 180 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLN E 171 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 182 " --> pdb=" O TRP E 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 187 through 188 removed outlier: 5.792A pdb=" N LEU E 180 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLN E 171 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 182 " --> pdb=" O TRP E 169 " (cutoff:3.500A) 88 hydrogen bonds defined for protein. 213 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: 0.46 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1025 1.35 - 1.47: 884 1.47 - 1.59: 1362 1.59 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3287 Sorted by residual: bond pdb=" CA THR C 470 " pdb=" CB THR C 470 " ideal model delta sigma weight residual 1.528 1.583 -0.055 2.61e-02 1.47e+03 4.40e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" C3 NAG C1301 " pdb=" O3 NAG C1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.80e-01 bond pdb=" C2 NAG C1301 " pdb=" N2 NAG C1301 " ideal model delta sigma weight residual 1.439 1.457 -0.018 2.00e-02 2.50e+03 7.88e-01 ... (remaining 3282 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 4282 1.24 - 2.49: 139 2.49 - 3.73: 32 3.73 - 4.98: 8 4.98 - 6.22: 2 Bond angle restraints: 4463 Sorted by residual: angle pdb=" N SER E 140 " pdb=" CA SER E 140 " pdb=" C SER E 140 " ideal model delta sigma weight residual 109.81 116.03 -6.22 2.21e+00 2.05e-01 7.92e+00 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.60 112.37 -3.77 1.46e+00 4.69e-01 6.67e+00 angle pdb=" CA LYS C 386 " pdb=" CB LYS C 386 " pdb=" CG LYS C 386 " ideal model delta sigma weight residual 114.10 118.22 -4.12 2.00e+00 2.50e-01 4.25e+00 angle pdb=" N GLY E 198 " pdb=" CA GLY E 198 " pdb=" C GLY E 198 " ideal model delta sigma weight residual 110.90 114.03 -3.13 1.53e+00 4.27e-01 4.18e+00 angle pdb=" N SER E 35 " pdb=" CA SER E 35 " pdb=" C SER E 35 " ideal model delta sigma weight residual 108.55 111.69 -3.14 1.62e+00 3.81e-01 3.75e+00 ... (remaining 4458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 1748 16.77 - 33.55: 154 33.55 - 50.32: 37 50.32 - 67.09: 3 67.09 - 83.87: 1 Dihedral angle restraints: 1943 sinusoidal: 764 harmonic: 1179 Sorted by residual: dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 142.95 -49.95 1 1.00e+01 1.00e-02 3.42e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 95 " pdb=" CB CYS E 95 " ideal model delta sinusoidal sigma weight residual -86.00 -128.20 42.20 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CA SER E 140 " pdb=" C SER E 140 " pdb=" N PRO E 141 " pdb=" CA PRO E 141 " ideal model delta harmonic sigma weight residual -180.00 -156.80 -23.20 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 1940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 327 0.034 - 0.069: 100 0.069 - 0.103: 37 0.103 - 0.137: 16 0.137 - 0.171: 1 Chirality restraints: 481 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA SER E 228 " pdb=" N SER E 228 " pdb=" C SER E 228 " pdb=" CB SER E 228 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE E 182 " pdb=" N ILE E 182 " pdb=" C ILE E 182 " pdb=" CB ILE E 182 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 478 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 147 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO E 148 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 148 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 148 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 140 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO E 141 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 141 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 141 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 498 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO C 499 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " 0.017 5.00e-02 4.00e+02 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 126 2.72 - 3.27: 3136 3.27 - 3.81: 4692 3.81 - 4.36: 5568 4.36 - 4.90: 9744 Nonbonded interactions: 23266 Sorted by model distance: nonbonded pdb=" OG SER E 147 " pdb=" OE1 GLU E 150 " model vdw 2.176 3.040 nonbonded pdb=" O ALA C 475 " pdb=" OG1 THR E 28 " model vdw 2.186 3.040 nonbonded pdb=" OG SER E 159 " pdb=" OE1 GLN E 160 " model vdw 2.206 3.040 nonbonded pdb=" O ALA E 104 " pdb=" OH TYR E 170 " model vdw 2.212 3.040 nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.286 3.040 ... (remaining 23261 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=0.00 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: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.990 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.003 0.055 3294 Z= 0.120 Angle : 0.592 6.986 4478 Z= 0.311 Chirality : 0.042 0.171 481 Planarity : 0.004 0.036 578 Dihedral : 12.554 83.866 1181 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.40), residues: 404 helix: -4.11 (0.47), residues: 20 sheet: 0.12 (0.52), residues: 112 loop : -1.33 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 19 TYR 0.011 0.001 TYR E 225 PHE 0.014 0.001 PHE C 429 TRP 0.008 0.001 TRP E 169 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3287) covalent geometry : angle 0.57633 ( 4463) SS BOND : bond 0.00349 ( 6) SS BOND : angle 0.78810 ( 12) hydrogen bonds : bond 0.29890 ( 79) hydrogen bonds : angle 10.79930 ( 213) link_NAG-ASN : bond 0.00096 ( 1) link_NAG-ASN : angle 5.16495 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: E 89 ASP cc_start: 0.8686 (m-30) cc_final: 0.8345 (m-30) REVERT: E 238 ARG cc_start: 0.7467 (pmt170) cc_final: 0.6991 (ptp90) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0710 time to fit residues: 6.5995 Evaluate side-chains 64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 139 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 = 0.3560 r_free = 0.3560 target = 0.132716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114050 restraints weight = 6200.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115740 restraints weight = 4564.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117105 restraints weight = 3704.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117848 restraints weight = 3202.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118575 restraints weight = 2886.387| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3294 Z= 0.142 Angle : 0.599 6.201 4478 Z= 0.314 Chirality : 0.044 0.153 481 Planarity : 0.004 0.037 578 Dihedral : 5.650 54.091 476 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.32 % Allowed : 11.59 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.39), residues: 404 helix: -3.96 (0.54), residues: 23 sheet: 0.24 (0.46), residues: 123 loop : -1.25 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 19 TYR 0.017 0.001 TYR C 473 PHE 0.014 0.002 PHE E 205 TRP 0.012 0.001 TRP C 436 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3287) covalent geometry : angle 0.59289 ( 4463) SS BOND : bond 0.00574 ( 6) SS BOND : angle 1.13341 ( 12) hydrogen bonds : bond 0.04103 ( 79) hydrogen bonds : angle 7.29549 ( 213) link_NAG-ASN : bond 0.00003 ( 1) link_NAG-ASN : angle 2.60574 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.139 Fit side-chains REVERT: C 357 ARG cc_start: 0.7439 (mtp85) cc_final: 0.6310 (mtm180) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 0.0549 time to fit residues: 4.4297 Evaluate side-chains 62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain E residue 135 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0020 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 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 = 0.3546 r_free = 0.3546 target = 0.131077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111375 restraints weight = 6370.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113477 restraints weight = 4670.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115050 restraints weight = 3728.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115965 restraints weight = 3159.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116777 restraints weight = 2823.950| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3294 Z= 0.136 Angle : 0.576 6.202 4478 Z= 0.302 Chirality : 0.043 0.146 481 Planarity : 0.004 0.036 578 Dihedral : 5.624 54.439 476 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.06 % Allowed : 12.17 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.40), residues: 404 helix: -3.83 (0.59), residues: 23 sheet: 0.33 (0.46), residues: 127 loop : -1.26 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 466 TYR 0.010 0.001 TYR C 453 PHE 0.014 0.001 PHE E 205 TRP 0.008 0.001 TRP C 436 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3287) covalent geometry : angle 0.57314 ( 4463) SS BOND : bond 0.00522 ( 6) SS BOND : angle 1.02884 ( 12) hydrogen bonds : bond 0.03594 ( 79) hydrogen bonds : angle 6.57243 ( 213) link_NAG-ASN : bond 0.00126 ( 1) link_NAG-ASN : angle 1.77772 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: C 357 ARG cc_start: 0.7499 (mtp85) cc_final: 0.6350 (mtm180) REVERT: E 155 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6970 (m-80) outliers start: 14 outliers final: 8 residues processed: 70 average time/residue: 0.0733 time to fit residues: 6.1387 Evaluate side-chains 69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 209 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 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 = 0.3545 r_free = 0.3545 target = 0.131171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111925 restraints weight = 6251.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113874 restraints weight = 4610.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115145 restraints weight = 3730.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116249 restraints weight = 3211.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116884 restraints weight = 2866.273| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3294 Z= 0.137 Angle : 0.579 6.323 4478 Z= 0.303 Chirality : 0.043 0.158 481 Planarity : 0.004 0.036 578 Dihedral : 5.615 54.304 476 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.61 % Allowed : 15.94 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.40), residues: 404 helix: -3.72 (0.66), residues: 23 sheet: 0.37 (0.47), residues: 127 loop : -1.32 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 509 TYR 0.016 0.001 TYR C 473 PHE 0.011 0.001 PHE E 155 TRP 0.008 0.001 TRP C 436 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3287) covalent geometry : angle 0.57654 ( 4463) SS BOND : bond 0.00506 ( 6) SS BOND : angle 1.00461 ( 12) hydrogen bonds : bond 0.03504 ( 79) hydrogen bonds : angle 6.39055 ( 213) link_NAG-ASN : bond 0.00116 ( 1) link_NAG-ASN : angle 1.41796 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: C 357 ARG cc_start: 0.7460 (mtp85) cc_final: 0.6295 (mtm180) REVERT: E 238 ARG cc_start: 0.7420 (pmt170) cc_final: 0.7048 (mtm-85) outliers start: 9 outliers final: 7 residues processed: 68 average time/residue: 0.0757 time to fit residues: 6.1044 Evaluate side-chains 63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 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 = 0.3515 r_free = 0.3515 target = 0.129832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111824 restraints weight = 6070.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113551 restraints weight = 4535.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114831 restraints weight = 3685.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115715 restraints weight = 3173.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116175 restraints weight = 2840.622| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3294 Z= 0.166 Angle : 0.593 6.474 4478 Z= 0.312 Chirality : 0.043 0.147 481 Planarity : 0.004 0.036 578 Dihedral : 5.772 54.522 476 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.19 % Allowed : 15.65 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.40), residues: 404 helix: -3.77 (0.64), residues: 23 sheet: 0.39 (0.46), residues: 132 loop : -1.36 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 238 TYR 0.012 0.001 TYR C 453 PHE 0.010 0.001 PHE E 155 TRP 0.007 0.001 TRP C 436 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3287) covalent geometry : angle 0.59001 ( 4463) SS BOND : bond 0.00535 ( 6) SS BOND : angle 1.14511 ( 12) hydrogen bonds : bond 0.03582 ( 79) hydrogen bonds : angle 6.35833 ( 213) link_NAG-ASN : bond 0.00111 ( 1) link_NAG-ASN : angle 1.36443 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8472 (mttp) cc_final: 0.7846 (mmtm) REVERT: C 423 TYR cc_start: 0.8954 (t80) cc_final: 0.8703 (t80) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.0702 time to fit residues: 5.7822 Evaluate side-chains 61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** E 139 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 = 0.3521 r_free = 0.3521 target = 0.130407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112933 restraints weight = 6053.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114499 restraints weight = 4572.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115735 restraints weight = 3764.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116360 restraints weight = 3261.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117180 restraints weight = 2970.536| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3294 Z= 0.133 Angle : 0.577 6.353 4478 Z= 0.301 Chirality : 0.042 0.138 481 Planarity : 0.004 0.033 578 Dihedral : 5.652 54.248 476 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.64 % Allowed : 15.94 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.40), residues: 404 helix: -3.70 (0.68), residues: 23 sheet: 0.40 (0.47), residues: 133 loop : -1.36 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 238 TYR 0.021 0.001 TYR C 473 PHE 0.017 0.001 PHE E 205 TRP 0.009 0.001 TRP C 436 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3287) covalent geometry : angle 0.57448 ( 4463) SS BOND : bond 0.00512 ( 6) SS BOND : angle 1.04872 ( 12) hydrogen bonds : bond 0.03199 ( 79) hydrogen bonds : angle 6.14635 ( 213) link_NAG-ASN : bond 0.00146 ( 1) link_NAG-ASN : angle 1.28668 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8406 (mttp) cc_final: 0.7871 (mmtm) REVERT: E 238 ARG cc_start: 0.7570 (pmt170) cc_final: 0.7134 (mtm-85) outliers start: 16 outliers final: 9 residues processed: 69 average time/residue: 0.0657 time to fit residues: 5.5511 Evaluate side-chains 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116669 restraints weight = 6109.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116974 restraints weight = 4475.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117398 restraints weight = 4499.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117765 restraints weight = 3828.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118040 restraints weight = 3572.358| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3294 Z= 0.111 Angle : 0.574 6.153 4478 Z= 0.298 Chirality : 0.042 0.134 481 Planarity : 0.004 0.034 578 Dihedral : 5.463 54.319 476 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.77 % Allowed : 16.81 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.40), residues: 404 helix: -3.61 (0.73), residues: 23 sheet: 0.65 (0.49), residues: 123 loop : -1.35 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 355 TYR 0.011 0.001 TYR E 170 PHE 0.012 0.001 PHE E 205 TRP 0.009 0.001 TRP C 436 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3287) covalent geometry : angle 0.57182 ( 4463) SS BOND : bond 0.00478 ( 6) SS BOND : angle 0.93210 ( 12) hydrogen bonds : bond 0.02871 ( 79) hydrogen bonds : angle 5.88396 ( 213) link_NAG-ASN : bond 0.00069 ( 1) link_NAG-ASN : angle 1.39144 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8379 (mttp) cc_final: 0.7831 (mmtm) REVERT: E 238 ARG cc_start: 0.7258 (pmt170) cc_final: 0.7011 (mtm-85) outliers start: 13 outliers final: 8 residues processed: 66 average time/residue: 0.0744 time to fit residues: 5.8754 Evaluate side-chains 62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 2 optimal weight: 0.0170 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 35 optimal weight: 0.0470 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN C 501 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116025 restraints weight = 6204.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117803 restraints weight = 4540.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119288 restraints weight = 3655.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.120178 restraints weight = 3104.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120955 restraints weight = 2757.532| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3294 Z= 0.105 Angle : 0.572 8.446 4478 Z= 0.293 Chirality : 0.042 0.132 481 Planarity : 0.004 0.033 578 Dihedral : 5.345 54.054 476 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.90 % Allowed : 17.39 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.41), residues: 404 helix: -3.53 (0.75), residues: 23 sheet: 0.81 (0.49), residues: 129 loop : -1.41 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 355 TYR 0.011 0.001 TYR E 170 PHE 0.008 0.001 PHE E 205 TRP 0.009 0.001 TRP C 436 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3287) covalent geometry : angle 0.57009 ( 4463) SS BOND : bond 0.00448 ( 6) SS BOND : angle 0.85046 ( 12) hydrogen bonds : bond 0.02723 ( 79) hydrogen bonds : angle 5.75521 ( 213) link_NAG-ASN : bond 0.00135 ( 1) link_NAG-ASN : angle 1.43504 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8355 (mttp) cc_final: 0.7761 (mmtm) REVERT: E 169 TRP cc_start: 0.8880 (m100) cc_final: 0.8665 (m100) REVERT: E 205 PHE cc_start: 0.8209 (m-10) cc_final: 0.7772 (m-10) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 0.0702 time to fit residues: 5.8604 Evaluate side-chains 62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.0170 chunk 1 optimal weight: 0.0060 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 ASN C 450 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113135 restraints weight = 6173.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114841 restraints weight = 4566.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116269 restraints weight = 3694.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117166 restraints weight = 3152.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117904 restraints weight = 2818.815| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3294 Z= 0.144 Angle : 0.608 6.510 4478 Z= 0.314 Chirality : 0.043 0.137 481 Planarity : 0.004 0.032 578 Dihedral : 5.515 54.321 476 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.77 % Allowed : 17.97 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.41), residues: 404 helix: -3.56 (0.72), residues: 23 sheet: 0.66 (0.48), residues: 128 loop : -1.32 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 19 TYR 0.028 0.001 TYR C 473 PHE 0.010 0.001 PHE E 205 TRP 0.007 0.001 TRP C 436 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3287) covalent geometry : angle 0.60559 ( 4463) SS BOND : bond 0.00474 ( 6) SS BOND : angle 0.96134 ( 12) hydrogen bonds : bond 0.03007 ( 79) hydrogen bonds : angle 5.89575 ( 213) link_NAG-ASN : bond 0.00109 ( 1) link_NAG-ASN : angle 1.54480 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8444 (mttp) cc_final: 0.7859 (mmtm) REVERT: E 169 TRP cc_start: 0.8863 (m100) cc_final: 0.8652 (m100) outliers start: 13 outliers final: 11 residues processed: 65 average time/residue: 0.0721 time to fit residues: 5.6256 Evaluate side-chains 66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN ** C 506 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 = 0.3590 r_free = 0.3590 target = 0.135264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117399 restraints weight = 6122.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119344 restraints weight = 4437.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120571 restraints weight = 3539.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121663 restraints weight = 3024.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122331 restraints weight = 2688.978| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3294 Z= 0.107 Angle : 0.595 6.640 4478 Z= 0.305 Chirality : 0.042 0.133 481 Planarity : 0.004 0.034 578 Dihedral : 5.321 53.613 476 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.77 % Allowed : 18.26 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.41), residues: 404 helix: -3.40 (0.79), residues: 23 sheet: 0.70 (0.49), residues: 123 loop : -1.23 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 19 TYR 0.025 0.001 TYR C 473 PHE 0.014 0.001 PHE E 205 TRP 0.010 0.001 TRP C 436 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3287) covalent geometry : angle 0.59354 ( 4463) SS BOND : bond 0.00441 ( 6) SS BOND : angle 0.85601 ( 12) hydrogen bonds : bond 0.02620 ( 79) hydrogen bonds : angle 5.58696 ( 213) link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 1.35443 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8309 (mttp) cc_final: 0.7742 (mmtm) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.0664 time to fit residues: 5.5703 Evaluate side-chains 66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN ** C 506 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 = 0.3542 r_free = 0.3542 target = 0.131633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113442 restraints weight = 6200.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115350 restraints weight = 4515.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116724 restraints weight = 3626.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117730 restraints weight = 3087.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118399 restraints weight = 2740.261| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3294 Z= 0.138 Angle : 0.631 8.151 4478 Z= 0.322 Chirality : 0.043 0.130 481 Planarity : 0.004 0.032 578 Dihedral : 5.502 54.081 476 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.19 % Allowed : 19.71 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.41), residues: 404 helix: -3.47 (0.74), residues: 23 sheet: 0.78 (0.49), residues: 119 loop : -1.26 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 19 TYR 0.027 0.001 TYR C 473 PHE 0.015 0.001 PHE E 205 TRP 0.042 0.003 TRP E 169 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3287) covalent geometry : angle 0.62827 ( 4463) SS BOND : bond 0.00450 ( 6) SS BOND : angle 1.12774 ( 12) hydrogen bonds : bond 0.02945 ( 79) hydrogen bonds : angle 5.82682 ( 213) link_NAG-ASN : bond 0.00082 ( 1) link_NAG-ASN : angle 1.54786 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 805.15 seconds wall clock time: 14 minutes 30.69 seconds (870.69 seconds total)