Starting phenix.real_space_refine on Mon Jan 13 16:15:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgr_50418/01_2025/9fgr_50418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgr_50418/01_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_50418/01_2025/9fgr_50418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgr_50418/01_2025/9fgr_50418.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgr_50418/01_2025/9fgr_50418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgr_50418/01_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-5571/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: 3.79, per 1000 atoms: 1.18 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: 0.76 Conformation dependent library (CDL) restraints added in 417.9 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: 0.38 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: 0.95 Time building geometry restraints manager: 0.90 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: 2.720 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.880 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- 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 : 0.387 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: 0.1716 time to fit residues: 16.0612 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 : 0.365 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.132406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113575 restraints weight = 6123.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115384 restraints weight = 4625.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116563 restraints weight = 3772.705| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.375 Fit side-chains REVERT: C 357 ARG cc_start: 0.7483 (mtp85) cc_final: 0.6335 (mtm180) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.1658 time to fit residues: 13.1003 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 : 0.346 ------------------------------------------------------------------------------- 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: 0.0470 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: 0.9980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.0080 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.127986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108551 restraints weight = 6333.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110504 restraints weight = 4632.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111764 restraints weight = 3728.584| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3287 Z= 0.315 Angle : 0.628 6.236 4463 Z= 0.334 Chirality : 0.044 0.149 481 Planarity : 0.004 0.037 578 Dihedral : 5.987 54.317 476 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.19 % Allowed : 13.33 % Favored : 83.48 % 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: -1.54 (0.39), residues: 404 helix: -3.95 (0.54), residues: 23 sheet: 0.11 (0.45), residues: 132 loop : -1.42 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.013 0.002 PHE E 205 TYR 0.016 0.002 TYR C 453 ARG 0.003 0.001 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 70 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.376 Fit side-chains REVERT: C 378 LYS cc_start: 0.8603 (mttp) cc_final: 0.7917 (mmtm) REVERT: E 88 GLU cc_start: 0.7557 (pp20) cc_final: 0.7326 (pp20) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.1808 time to fit residues: 14.2773 Evaluate side-chains 60 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 0.8980 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.130324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112727 restraints weight = 6041.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114401 restraints weight = 4533.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115495 restraints weight = 3706.362| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2445 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= 0.216 Angle : 0.578 6.509 4463 Z= 0.305 Chirality : 0.043 0.142 481 Planarity : 0.004 0.036 578 Dihedral : 5.760 54.418 476 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.61 % Allowed : 14.78 % Favored : 82.61 % 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: -1.42 (0.40), residues: 404 helix: -3.76 (0.64), residues: 23 sheet: 0.26 (0.46), residues: 132 loop : -1.39 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 PHE 0.011 0.001 PHE E 155 TYR 0.022 0.001 TYR C 473 ARG 0.002 0.000 ARG E 238 *********************** 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 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8432 (mttp) cc_final: 0.7891 (mmtm) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.1859 time to fit residues: 13.8503 Evaluate side-chains 59 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.0020 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 ** 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 = 0.3515 r_free = 0.3515 target = 0.130060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112146 restraints weight = 6025.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113920 restraints weight = 4490.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.115056 restraints weight = 3633.769| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2499 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= 0.225 Angle : 0.578 6.413 4463 Z= 0.304 Chirality : 0.043 0.138 481 Planarity : 0.004 0.035 578 Dihedral : 5.695 54.348 476 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % 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: -1.38 (0.40), residues: 404 helix: -3.74 (0.65), residues: 23 sheet: 0.34 (0.46), residues: 132 loop : -1.40 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.011 0.001 PHE E 155 TYR 0.010 0.001 TYR C 453 ARG 0.002 0.000 ARG E 238 *********************** 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 : 0.363 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8445 (mttp) cc_final: 0.7868 (mmtm) outliers start: 11 outliers final: 10 residues processed: 68 average time/residue: 0.1663 time to fit residues: 13.6818 Evaluate side-chains 64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.0010 chunk 25 optimal weight: 0.8980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN 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 = 0.3534 r_free = 0.3534 target = 0.131223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113741 restraints weight = 6164.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115443 restraints weight = 4574.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116148 restraints weight = 3708.636| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3287 Z= 0.192 Angle : 0.565 6.292 4463 Z= 0.295 Chirality : 0.042 0.135 481 Planarity : 0.004 0.034 578 Dihedral : 5.607 54.267 476 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.35 % Allowed : 17.10 % Favored : 78.55 % 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: -1.36 (0.40), residues: 404 helix: -3.66 (0.69), residues: 23 sheet: 0.49 (0.48), residues: 127 loop : -1.44 (0.36), residues: 254 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 0.028 0.001 TYR C 473 ARG 0.002 0.000 ARG E 238 *********************** 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 69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8411 (mttp) cc_final: 0.7870 (mmtm) REVERT: E 88 GLU cc_start: 0.7701 (pp20) cc_final: 0.7483 (pp20) outliers start: 15 outliers final: 9 residues processed: 68 average time/residue: 0.1566 time to fit residues: 13.1843 Evaluate side-chains 62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 228 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.0060 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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** 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 = 0.3540 r_free = 0.3540 target = 0.131772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115740 restraints weight = 6023.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115952 restraints weight = 4390.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116152 restraints weight = 4366.810| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3287 Z= 0.194 Angle : 0.578 6.321 4463 Z= 0.298 Chirality : 0.042 0.138 481 Planarity : 0.004 0.033 578 Dihedral : 5.557 54.389 476 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.64 % Allowed : 17.10 % 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: -1.26 (0.40), residues: 404 helix: -3.60 (0.72), residues: 23 sheet: 0.73 (0.49), residues: 122 loop : -1.44 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.012 0.001 PHE E 205 TYR 0.023 0.001 TYR C 473 ARG 0.002 0.000 ARG E 238 *********************** 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 71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8424 (mttp) cc_final: 0.7880 (mmtm) REVERT: E 88 GLU cc_start: 0.7809 (pp20) cc_final: 0.7535 (pp20) outliers start: 16 outliers final: 10 residues processed: 70 average time/residue: 0.1637 time to fit residues: 13.9311 Evaluate side-chains 62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 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 = 0.3550 r_free = 0.3550 target = 0.132447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114650 restraints weight = 6095.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116573 restraints weight = 4484.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117787 restraints weight = 3582.021| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2845 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= 0.176 Angle : 0.561 6.165 4463 Z= 0.290 Chirality : 0.042 0.137 481 Planarity : 0.004 0.033 578 Dihedral : 5.485 54.001 476 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % 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: -1.21 (0.41), residues: 404 helix: -3.51 (0.75), residues: 23 sheet: 0.79 (0.49), residues: 128 loop : -1.48 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 PHE 0.010 0.001 PHE E 205 TYR 0.010 0.001 TYR E 170 ARG 0.005 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: 11 poor density : 57 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8418 (mttp) cc_final: 0.7829 (mmtm) REVERT: E 88 GLU cc_start: 0.7777 (pp20) cc_final: 0.7533 (pp20) REVERT: E 224 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8065 (tm-30) outliers start: 11 outliers final: 9 residues processed: 66 average time/residue: 0.1506 time to fit residues: 12.1783 Evaluate side-chains 63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.0020 chunk 34 optimal weight: 0.2980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.132718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115128 restraints weight = 6056.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116856 restraints weight = 4444.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118268 restraints weight = 3582.982| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3287 Z= 0.184 Angle : 0.594 7.926 4463 Z= 0.301 Chirality : 0.042 0.137 481 Planarity : 0.004 0.033 578 Dihedral : 5.473 54.113 476 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.48 % Allowed : 18.26 % 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: -1.22 (0.41), residues: 404 helix: -3.49 (0.76), residues: 23 sheet: 0.72 (0.49), residues: 129 loop : -1.45 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.017 0.001 PHE E 205 TYR 0.011 0.001 TYR E 52 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: 12 poor density : 59 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8408 (mttp) cc_final: 0.7831 (mmtm) REVERT: E 88 GLU cc_start: 0.7810 (pp20) cc_final: 0.7583 (pp20) REVERT: E 167 LEU cc_start: 0.9035 (tt) cc_final: 0.8777 (tt) REVERT: E 205 PHE cc_start: 0.8149 (m-10) cc_final: 0.7885 (m-10) outliers start: 12 outliers final: 11 residues processed: 69 average time/residue: 0.1481 time to fit residues: 12.5823 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 : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 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 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 = 0.3536 r_free = 0.3536 target = 0.131348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113462 restraints weight = 6045.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115320 restraints weight = 4399.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116666 restraints weight = 3545.574| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3287 Z= 0.217 Angle : 0.614 7.450 4463 Z= 0.314 Chirality : 0.043 0.132 481 Planarity : 0.004 0.033 578 Dihedral : 5.563 54.245 476 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.48 % Allowed : 18.84 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.30 (0.40), residues: 404 helix: -3.51 (0.74), residues: 23 sheet: 0.64 (0.49), residues: 122 loop : -1.44 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP E 169 PHE 0.017 0.001 PHE E 205 TYR 0.014 0.001 TYR E 52 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 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8452 (mttp) cc_final: 0.7858 (mmtm) REVERT: E 82 MET cc_start: 0.7999 (mtt) cc_final: 0.7698 (mtt) REVERT: E 88 GLU cc_start: 0.7871 (pp20) cc_final: 0.7577 (pp20) REVERT: E 205 PHE cc_start: 0.8223 (m-10) cc_final: 0.7914 (m-10) outliers start: 12 outliers final: 11 residues processed: 62 average time/residue: 0.1495 time to fit residues: 11.5021 Evaluate side-chains 64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER 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 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 8 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.0570 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.0270 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.132384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114570 restraints weight = 6059.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116292 restraints weight = 4405.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117731 restraints weight = 3552.933| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3044 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= 0.184 Angle : 0.586 6.988 4463 Z= 0.303 Chirality : 0.042 0.131 481 Planarity : 0.004 0.033 578 Dihedral : 5.489 53.770 476 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.19 % Allowed : 19.13 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.27 (0.41), residues: 404 helix: -3.61 (0.71), residues: 23 sheet: 0.56 (0.49), residues: 123 loop : -1.35 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 169 PHE 0.015 0.001 PHE E 205 TYR 0.012 0.001 TYR E 170 ARG 0.003 0.000 ARG E 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1470.98 seconds wall clock time: 27 minutes 27.94 seconds (1647.94 seconds total)