Starting phenix.real_space_refine on Wed Mar 5 18:12:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgr_50418/03_2025/9fgr_50418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgr_50418/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fgr_50418/03_2025/9fgr_50418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgr_50418/03_2025/9fgr_50418.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgr_50418/03_2025/9fgr_50418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgr_50418/03_2025/9fgr_50418.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.56, per 1000 atoms: 1.11 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: 0.79 Conformation dependent library (CDL) restraints added in 403.7 milliseconds 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: 0.47 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: 0.85 Time building geometry restraints manager: 0.95 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.050 Find NCS groups from input model: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.970 ------------------------------------------------------------------------------- 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 3287 Z= 0.171 Angle : 0.576 6.219 4463 Z= 0.308 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.001 TRP E 169 PHE 0.014 0.001 PHE C 429 TYR 0.011 0.001 TYR E 225 ARG 0.002 0.000 ARG E 19 *********************** 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 : 0.386 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: 0.1724 time to fit residues: 16.1326 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 : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.132196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113568 restraints weight = 6061.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115268 restraints weight = 4483.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116603 restraints weight = 3648.754| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3287 Z= 0.203 Angle : 0.587 6.053 4463 Z= 0.309 Chirality : 0.044 0.151 481 Planarity : 0.004 0.036 578 Dihedral : 5.623 54.070 476 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.48 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.40), residues: 404 helix: -3.95 (0.54), residues: 23 sheet: 0.26 (0.46), residues: 123 loop : -1.23 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 PHE 0.015 0.001 PHE E 205 TYR 0.016 0.001 TYR C 473 ARG 0.002 0.000 ARG E 19 *********************** 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 70 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.387 Fit side-chains REVERT: C 357 ARG cc_start: 0.7484 (mtp85) cc_final: 0.6335 (mtm180) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.1678 time to fit residues: 13.2088 Evaluate side-chains 60 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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: 0.0030 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.131230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112380 restraints weight = 6284.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114283 restraints weight = 4599.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115531 restraints weight = 3696.411| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3287 Z= 0.211 Angle : 0.573 6.211 4463 Z= 0.300 Chirality : 0.043 0.146 481 Planarity : 0.004 0.036 578 Dihedral : 5.614 54.363 476 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.77 % Allowed : 12.17 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.40), residues: 404 helix: -3.81 (0.59), residues: 23 sheet: 0.36 (0.46), residues: 127 loop : -1.26 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.015 0.001 PHE E 205 TYR 0.010 0.001 TYR C 453 ARG 0.002 0.000 ARG E 238 *********************** 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 74 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: C 357 ARG cc_start: 0.7531 (mtp85) cc_final: 0.6367 (mtm180) REVERT: E 155 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6986 (m-80) outliers start: 13 outliers final: 6 residues processed: 72 average time/residue: 0.1797 time to fit residues: 15.4259 Evaluate side-chains 67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 73 ASN ** 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 = 0.3533 r_free = 0.3533 target = 0.130345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110963 restraints weight = 6302.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112858 restraints weight = 4681.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114120 restraints weight = 3808.594| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3287 Z= 0.220 Angle : 0.579 6.452 4463 Z= 0.304 Chirality : 0.043 0.149 481 Planarity : 0.004 0.035 578 Dihedral : 5.638 54.297 476 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.03 % Allowed : 16.23 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.40), residues: 404 helix: -3.71 (0.67), residues: 23 sheet: 0.40 (0.47), residues: 127 loop : -1.33 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.011 0.001 PHE E 205 TYR 0.017 0.001 TYR C 473 ARG 0.002 0.000 ARG C 509 *********************** 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 70 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: E 238 ARG cc_start: 0.7486 (pmt170) cc_final: 0.7051 (mtm-85) outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 0.2004 time to fit residues: 16.0796 Evaluate side-chains 62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 20 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.132953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116665 restraints weight = 5971.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116969 restraints weight = 4387.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117074 restraints weight = 4323.098| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3287 Z= 0.172 Angle : 0.544 6.315 4463 Z= 0.284 Chirality : 0.042 0.156 481 Planarity : 0.004 0.033 578 Dihedral : 5.452 54.126 476 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.48 % Allowed : 15.65 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.40), residues: 404 helix: -3.61 (0.72), residues: 23 sheet: 0.48 (0.48), residues: 128 loop : -1.31 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 PHE 0.013 0.001 PHE E 205 TYR 0.008 0.001 TYR C 453 ARG 0.001 0.000 ARG C 457 *********************** 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 74 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: E 238 ARG cc_start: 0.7455 (pmt170) cc_final: 0.7096 (mtm-85) outliers start: 12 outliers final: 7 residues processed: 71 average time/residue: 0.1671 time to fit residues: 14.3049 Evaluate side-chains 64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3526 r_free = 0.3526 target = 0.130662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114377 restraints weight = 6170.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114650 restraints weight = 4490.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114977 restraints weight = 4472.027| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3287 Z= 0.216 Angle : 0.586 6.287 4463 Z= 0.305 Chirality : 0.043 0.140 481 Planarity : 0.004 0.034 578 Dihedral : 5.552 54.205 476 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.48 % Allowed : 16.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.40), residues: 404 helix: -3.65 (0.69), residues: 23 sheet: 0.63 (0.48), residues: 127 loop : -1.35 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 PHE 0.010 0.001 PHE E 205 TYR 0.011 0.001 TYR C 423 ARG 0.004 0.000 ARG E 19 *********************** 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 72 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: E 238 ARG cc_start: 0.7423 (pmt170) cc_final: 0.7025 (mtm-85) outliers start: 12 outliers final: 8 residues processed: 70 average time/residue: 0.1802 time to fit residues: 15.2968 Evaluate side-chains 64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 228 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3523 r_free = 0.3523 target = 0.130548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114206 restraints weight = 6075.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114492 restraints weight = 4444.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114828 restraints weight = 4433.672| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3287 Z= 0.230 Angle : 0.610 7.172 4463 Z= 0.315 Chirality : 0.043 0.138 481 Planarity : 0.004 0.034 578 Dihedral : 5.680 54.697 476 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.19 % Allowed : 17.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.41), residues: 404 helix: -3.62 (0.70), residues: 23 sheet: 0.81 (0.48), residues: 127 loop : -1.38 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 PHE 0.009 0.001 PHE C 342 TYR 0.014 0.001 TYR E 170 ARG 0.004 0.000 ARG E 19 *********************** 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 72 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8421 (mttp) cc_final: 0.7884 (mmtm) REVERT: E 205 PHE cc_start: 0.8376 (m-10) cc_final: 0.7797 (m-10) REVERT: E 238 ARG cc_start: 0.7359 (pmt170) cc_final: 0.7011 (mtm-85) outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 0.1627 time to fit residues: 13.9938 Evaluate side-chains 64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 155 PHE 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 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 36 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3553 r_free = 0.3553 target = 0.132717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114963 restraints weight = 6076.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116820 restraints weight = 4430.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118142 restraints weight = 3555.093| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3287 Z= 0.187 Angle : 0.586 6.655 4463 Z= 0.303 Chirality : 0.043 0.138 481 Planarity : 0.004 0.033 578 Dihedral : 5.495 54.043 476 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.90 % Allowed : 18.26 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.41), residues: 404 helix: -3.54 (0.75), residues: 23 sheet: 0.80 (0.48), residues: 129 loop : -1.41 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 PHE 0.012 0.001 PHE E 205 TYR 0.010 0.001 TYR E 52 ARG 0.003 0.000 ARG E 19 *********************** 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 68 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8424 (mttp) cc_final: 0.7844 (mmtm) REVERT: E 169 TRP cc_start: 0.8878 (m100) cc_final: 0.8642 (m100) REVERT: E 238 ARG cc_start: 0.7259 (pmt170) cc_final: 0.6998 (mtm-85) outliers start: 10 outliers final: 10 residues processed: 66 average time/residue: 0.1696 time to fit residues: 13.4675 Evaluate side-chains 67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 368 LEU 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 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE 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 38 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 29 optimal weight: 0.0170 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117398 restraints weight = 6000.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117697 restraints weight = 4395.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117873 restraints weight = 4377.811| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3287 Z= 0.181 Angle : 0.590 6.659 4463 Z= 0.306 Chirality : 0.043 0.136 481 Planarity : 0.004 0.033 578 Dihedral : 5.435 53.964 476 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.90 % Allowed : 18.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.41), residues: 404 helix: -3.47 (0.76), residues: 23 sheet: 0.79 (0.48), residues: 129 loop : -1.41 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.018 0.001 PHE E 205 TYR 0.027 0.001 TYR C 473 ARG 0.003 0.000 ARG E 19 *********************** 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 71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8364 (mttp) cc_final: 0.7815 (mmtm) REVERT: E 169 TRP cc_start: 0.8869 (m100) cc_final: 0.8626 (m100) REVERT: E 238 ARG cc_start: 0.7269 (pmt170) cc_final: 0.7052 (mtm-85) outliers start: 10 outliers final: 10 residues processed: 70 average time/residue: 0.1816 time to fit residues: 15.3757 Evaluate side-chains 67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 12 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 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 = 0.3539 r_free = 0.3539 target = 0.131491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113625 restraints weight = 6041.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115493 restraints weight = 4402.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116843 restraints weight = 3536.465| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3287 Z= 0.215 Angle : 0.595 6.705 4463 Z= 0.309 Chirality : 0.043 0.136 481 Planarity : 0.004 0.033 578 Dihedral : 5.581 54.061 476 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.19 % Allowed : 18.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.41), residues: 404 helix: -3.56 (0.71), residues: 23 sheet: 0.71 (0.47), residues: 129 loop : -1.42 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 PHE 0.017 0.001 PHE E 205 TYR 0.028 0.001 TYR C 473 ARG 0.004 0.000 ARG E 19 ********************** 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 67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: C 338 PHE cc_start: 0.7084 (p90) cc_final: 0.6793 (p90) REVERT: C 378 LYS cc_start: 0.8476 (mttp) cc_final: 0.7874 (mmtm) REVERT: E 169 TRP cc_start: 0.8904 (m100) cc_final: 0.8626 (m100) REVERT: E 238 ARG cc_start: 0.7430 (pmt170) cc_final: 0.7106 (mtm-85) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.1720 time to fit residues: 13.7365 Evaluate side-chains 66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.133155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117036 restraints weight = 5927.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117317 restraints weight = 4333.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117465 restraints weight = 4289.085| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3287 Z= 0.202 Angle : 0.613 8.222 4463 Z= 0.313 Chirality : 0.043 0.135 481 Planarity : 0.004 0.032 578 Dihedral : 5.524 53.745 476 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.19 % Allowed : 19.42 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.41), residues: 404 helix: -3.54 (0.73), residues: 23 sheet: 0.71 (0.47), residues: 129 loop : -1.40 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.014 0.001 PHE E 205 TYR 0.027 0.001 TYR C 473 ARG 0.004 0.000 ARG E 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.35 seconds wall clock time: 26 minutes 42.69 seconds (1602.69 seconds total)