Starting phenix.real_space_refine on Tue Feb 11 08:01:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eya_31380/02_2025/7eya_31380.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eya_31380/02_2025/7eya_31380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eya_31380/02_2025/7eya_31380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eya_31380/02_2025/7eya_31380.map" model { file = "/net/cci-nas-00/data/ceres_data/7eya_31380/02_2025/7eya_31380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eya_31380/02_2025/7eya_31380.cif" } resolution = 3.77 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= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2970 2.51 5 N 756 2.21 5 O 885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4629 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 801 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 965 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1359 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 7 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.39, per 1000 atoms: 0.95 Number of scatterers: 4629 At special positions: 0 Unit cell: (73.03, 95.92, 98.1, 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 18 16.00 O 885 8.00 N 756 7.00 C 2970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.05 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 166 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN N 165 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 742.1 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1066 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 11 sheets defined 9.4% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'R' and resid 337 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.533A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 390 removed outlier: 4.456A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 410 Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing helix chain 'R' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 4.287A pdb=" N ASN R 394 " --> pdb=" O GLU R 516 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU R 516 " --> pdb=" O ASN R 394 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.535A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.577A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.598A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.598A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.750A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 29 through 31 Processing sheet with id=AA9, first strand: chain 'N' and resid 50 through 51 removed outlier: 4.109A pdb=" N ASP N 287 " --> pdb=" O LYS N 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 84 through 85 removed outlier: 3.547A pdb=" N SER N 172 " --> pdb=" O VAL N 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 224 through 229 removed outlier: 5.988A pdb=" N SER N 205 " --> pdb=" O PRO N 225 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL N 227 " --> pdb=" O ILE N 203 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 303 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: 1.04 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 730 1.25 - 1.40: 1345 1.40 - 1.55: 2650 1.55 - 1.70: 1 1.70 - 1.84: 23 Bond restraints: 4749 Sorted by residual: bond pdb=" CG PRO R 507 " pdb=" CD PRO R 507 " ideal model delta sigma weight residual 1.503 1.107 0.396 3.40e-02 8.65e+02 1.36e+02 bond pdb=" CB PRO R 507 " pdb=" CG PRO R 507 " ideal model delta sigma weight residual 1.492 1.155 0.337 5.00e-02 4.00e+02 4.54e+01 bond pdb=" N PRO R 507 " pdb=" CD PRO R 507 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.80e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.553 -0.034 2.00e-02 2.50e+03 2.82e+00 bond pdb=" N PRO R 507 " pdb=" CA PRO R 507 " ideal model delta sigma weight residual 1.467 1.486 -0.019 1.21e-02 6.83e+03 2.55e+00 ... (remaining 4744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.20: 6441 9.20 - 18.40: 0 18.40 - 27.60: 2 27.60 - 36.80: 0 36.80 - 46.00: 1 Bond angle restraints: 6444 Sorted by residual: angle pdb=" N PRO R 507 " pdb=" CD PRO R 507 " pdb=" CG PRO R 507 " ideal model delta sigma weight residual 103.20 76.09 27.11 1.50e+00 4.44e-01 3.27e+02 angle pdb=" CB PRO R 507 " pdb=" CG PRO R 507 " pdb=" CD PRO R 507 " ideal model delta sigma weight residual 106.10 152.10 -46.00 3.20e+00 9.77e-02 2.07e+02 angle pdb=" CA PRO R 507 " pdb=" CB PRO R 507 " pdb=" CG PRO R 507 " ideal model delta sigma weight residual 104.50 79.51 24.99 1.90e+00 2.77e-01 1.73e+02 angle pdb=" CA PRO R 507 " pdb=" N PRO R 507 " pdb=" CD PRO R 507 " ideal model delta sigma weight residual 112.00 102.91 9.09 1.40e+00 5.10e-01 4.22e+01 angle pdb=" C ASN N 165 " pdb=" CA ASN N 165 " pdb=" CB ASN N 165 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 ... (remaining 6439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.17: 2587 22.17 - 44.34: 160 44.34 - 66.50: 21 66.50 - 88.67: 13 88.67 - 110.84: 12 Dihedral angle restraints: 2793 sinusoidal: 1120 harmonic: 1673 Sorted by residual: dihedral pdb=" CA PHE L 94 " pdb=" C PHE L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 134.96 45.04 0 5.00e+00 4.00e-02 8.12e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 164.63 -71.63 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual 180.00 140.26 39.74 0 5.00e+00 4.00e-02 6.32e+01 ... (remaining 2790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 584 0.054 - 0.109: 90 0.109 - 0.163: 21 0.163 - 0.217: 1 0.217 - 0.272: 1 Chirality restraints: 697 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA CYS N 166 " pdb=" N CYS N 166 " pdb=" C CYS N 166 " pdb=" CB CYS N 166 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CB VAL H 64 " pdb=" CA VAL H 64 " pdb=" CG1 VAL H 64 " pdb=" CG2 VAL H 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 694 not shown) Planarity restraints: 820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN R 506 " 0.057 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO R 507 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 507 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 507 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR N 38 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO N 39 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO N 39 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 39 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 94 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO L 95 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.037 5.00e-02 4.00e+02 ... (remaining 817 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 122 2.69 - 3.24: 4233 3.24 - 3.80: 6527 3.80 - 4.35: 8655 4.35 - 4.90: 14738 Nonbonded interactions: 34275 Sorted by model distance: nonbonded pdb=" OD1 ASP N 40 " pdb=" OH TYR N 204 " model vdw 2.142 3.040 nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.187 3.040 nonbonded pdb=" O GLN H 3 " pdb=" OG SER H 25 " model vdw 2.195 3.040 nonbonded pdb=" OD1 ASN R 439 " pdb=" OG SER R 443 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR N 91 " pdb=" OE1 GLU N 191 " model vdw 2.232 3.040 ... (remaining 34270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.910 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.980 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.008 0.396 4749 Z= 0.525 Angle : 1.005 46.004 6444 Z= 0.497 Chirality : 0.043 0.272 697 Planarity : 0.006 0.080 819 Dihedral : 16.975 110.839 1709 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.58 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.30 (0.35), residues: 554 helix: -2.80 (0.87), residues: 25 sheet: -0.56 (0.40), residues: 186 loop : -2.09 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.001 0.000 HIS H 59 PHE 0.013 0.001 PHE R 456 TYR 0.023 0.001 TYR H 102 ARG 0.004 0.000 ARG R 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.479 Fit side-chains REVERT: R 438 SER cc_start: 0.8217 (p) cc_final: 0.7686 (p) REVERT: H 83 MET cc_start: 0.6305 (ptt) cc_final: 0.6073 (ptt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1453 time to fit residues: 21.9172 Evaluate side-chains 94 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.0170 chunk 22 optimal weight: 0.0770 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 498 GLN H 3 GLN H 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.160378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137525 restraints weight = 6544.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140078 restraints weight = 9571.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141461 restraints weight = 6626.421| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4749 Z= 0.189 Angle : 0.670 9.172 6444 Z= 0.347 Chirality : 0.045 0.249 697 Planarity : 0.006 0.068 819 Dihedral : 12.329 84.867 694 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.04 % Favored : 92.78 % Rotamer: Outliers : 1.00 % Allowed : 9.36 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.13 (0.35), residues: 554 helix: -2.99 (0.88), residues: 25 sheet: -0.32 (0.41), residues: 181 loop : -2.00 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 35 HIS 0.001 0.000 HIS H 59 PHE 0.026 0.002 PHE N 43 TYR 0.016 0.001 TYR R 380 ARG 0.009 0.001 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.439 Fit side-chains REVERT: R 418 ILE cc_start: 0.9036 (tt) cc_final: 0.8755 (tt) REVERT: R 438 SER cc_start: 0.8049 (p) cc_final: 0.7524 (p) outliers start: 5 outliers final: 3 residues processed: 109 average time/residue: 0.1489 time to fit residues: 21.1498 Evaluate side-chains 100 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain N residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 53 optimal weight: 0.0050 chunk 54 optimal weight: 0.9980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 498 GLN H 3 GLN H 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.160471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.137619 restraints weight = 6505.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.139740 restraints weight = 8957.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.141292 restraints weight = 6794.372| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4749 Z= 0.174 Angle : 0.633 9.012 6444 Z= 0.324 Chirality : 0.045 0.267 697 Planarity : 0.005 0.066 819 Dihedral : 10.436 76.226 694 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 1.00 % Allowed : 13.55 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -1.98 (0.36), residues: 554 helix: -2.71 (1.18), residues: 19 sheet: -0.21 (0.40), residues: 187 loop : -1.97 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.002 0.000 HIS H 59 PHE 0.028 0.002 PHE R 456 TYR 0.016 0.001 TYR R 380 ARG 0.005 0.001 ARG R 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.512 Fit side-chains REVERT: R 418 ILE cc_start: 0.9159 (tt) cc_final: 0.8936 (tt) REVERT: R 438 SER cc_start: 0.8070 (p) cc_final: 0.7664 (p) REVERT: H 19 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7659 (mtp85) REVERT: N 32 PHE cc_start: 0.8125 (p90) cc_final: 0.7822 (p90) outliers start: 5 outliers final: 4 residues processed: 104 average time/residue: 0.1583 time to fit residues: 21.3790 Evaluate side-chains 99 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 498 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.158891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136001 restraints weight = 6596.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138094 restraints weight = 10166.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140061 restraints weight = 6283.098| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4749 Z= 0.202 Angle : 0.635 10.040 6444 Z= 0.324 Chirality : 0.045 0.269 697 Planarity : 0.005 0.068 819 Dihedral : 9.572 70.184 694 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.04 % Favored : 92.78 % Rotamer: Outliers : 1.59 % Allowed : 15.34 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -1.99 (0.36), residues: 554 helix: -2.54 (1.16), residues: 19 sheet: -0.36 (0.39), residues: 199 loop : -1.93 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 353 HIS 0.002 0.000 HIS H 59 PHE 0.044 0.002 PHE R 456 TYR 0.015 0.001 TYR H 95 ARG 0.004 0.001 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.485 Fit side-chains REVERT: R 418 ILE cc_start: 0.9163 (tt) cc_final: 0.8934 (tt) REVERT: R 438 SER cc_start: 0.8124 (p) cc_final: 0.7594 (p) REVERT: H 19 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7514 (mtp85) REVERT: N 169 GLU cc_start: 0.7493 (mp0) cc_final: 0.7011 (mp0) outliers start: 8 outliers final: 6 residues processed: 103 average time/residue: 0.1633 time to fit residues: 21.4318 Evaluate side-chains 99 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 52 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 498 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.160394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137280 restraints weight = 6678.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139927 restraints weight = 9867.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.141591 restraints weight = 5802.279| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4749 Z= 0.146 Angle : 0.613 9.132 6444 Z= 0.309 Chirality : 0.044 0.268 697 Planarity : 0.005 0.066 819 Dihedral : 8.952 65.386 694 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.68 % Favored : 93.14 % Rotamer: Outliers : 2.19 % Allowed : 16.14 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -1.95 (0.36), residues: 554 helix: -2.36 (1.15), residues: 19 sheet: -0.31 (0.39), residues: 204 loop : -1.96 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 3 HIS 0.001 0.000 HIS H 59 PHE 0.020 0.001 PHE N 43 TYR 0.013 0.001 TYR R 380 ARG 0.004 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.522 Fit side-chains REVERT: R 355 ARG cc_start: 0.7776 (ttt90) cc_final: 0.7424 (ttt90) REVERT: R 438 SER cc_start: 0.7912 (p) cc_final: 0.7356 (p) REVERT: L 36 TYR cc_start: 0.8810 (m-80) cc_final: 0.8545 (m-80) REVERT: H 19 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7562 (mtp85) REVERT: N 169 GLU cc_start: 0.7481 (mp0) cc_final: 0.7008 (mp0) outliers start: 11 outliers final: 8 residues processed: 105 average time/residue: 0.1453 time to fit residues: 19.8420 Evaluate side-chains 101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 23 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 3 optimal weight: 0.0020 chunk 0 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 437 ASN R 498 GLN H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.178896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153065 restraints weight = 6553.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156188 restraints weight = 7469.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.157754 restraints weight = 6341.585| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4749 Z= 0.168 Angle : 0.604 8.981 6444 Z= 0.307 Chirality : 0.044 0.246 697 Planarity : 0.005 0.067 819 Dihedral : 8.359 59.788 694 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.22 % Favored : 92.60 % Rotamer: Outliers : 2.39 % Allowed : 15.54 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -1.86 (0.36), residues: 554 helix: -2.22 (1.15), residues: 19 sheet: -0.29 (0.39), residues: 205 loop : -1.88 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 436 HIS 0.001 0.000 HIS H 59 PHE 0.024 0.001 PHE R 456 TYR 0.013 0.001 TYR H 95 ARG 0.003 0.000 ARG R 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.476 Fit side-chains REVERT: R 438 SER cc_start: 0.7865 (p) cc_final: 0.7304 (p) REVERT: L 36 TYR cc_start: 0.8842 (m-80) cc_final: 0.8606 (m-80) REVERT: H 19 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7467 (mtp85) REVERT: N 169 GLU cc_start: 0.7501 (mp0) cc_final: 0.6963 (mp0) outliers start: 12 outliers final: 11 residues processed: 103 average time/residue: 0.1397 time to fit residues: 19.0696 Evaluate side-chains 103 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 437 ASN R 498 GLN H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.177904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.153591 restraints weight = 6597.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155650 restraints weight = 8033.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.158237 restraints weight = 5994.175| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4749 Z= 0.197 Angle : 0.619 9.269 6444 Z= 0.315 Chirality : 0.044 0.238 697 Planarity : 0.006 0.072 819 Dihedral : 8.016 55.464 694 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.40 % Favored : 92.42 % Rotamer: Outliers : 2.79 % Allowed : 15.54 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -1.85 (0.36), residues: 554 helix: -0.98 (1.58), residues: 13 sheet: -0.36 (0.39), residues: 203 loop : -1.87 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 HIS 0.001 0.000 HIS H 59 PHE 0.023 0.001 PHE N 43 TYR 0.014 0.001 TYR H 95 ARG 0.003 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.539 Fit side-chains REVERT: R 438 SER cc_start: 0.7783 (p) cc_final: 0.7300 (p) REVERT: H 19 ARG cc_start: 0.7741 (mtm-85) cc_final: 0.7456 (mtp85) REVERT: N 58 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: N 169 GLU cc_start: 0.7502 (mp0) cc_final: 0.6954 (mp0) outliers start: 14 outliers final: 13 residues processed: 99 average time/residue: 0.1368 time to fit residues: 18.2471 Evaluate side-chains 103 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 498 GLN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 58 PHE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 0.0570 chunk 52 optimal weight: 0.4980 chunk 29 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 498 GLN H 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.176207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151114 restraints weight = 6580.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154036 restraints weight = 8631.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.156093 restraints weight = 5545.576| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4749 Z= 0.241 Angle : 0.645 9.438 6444 Z= 0.328 Chirality : 0.044 0.221 697 Planarity : 0.006 0.067 819 Dihedral : 7.694 50.666 694 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.22 % Favored : 92.60 % Rotamer: Outliers : 3.39 % Allowed : 15.34 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -1.86 (0.36), residues: 554 helix: -0.99 (1.57), residues: 13 sheet: -0.36 (0.39), residues: 203 loop : -1.89 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 353 HIS 0.002 0.000 HIS H 59 PHE 0.025 0.002 PHE N 43 TYR 0.017 0.001 TYR H 95 ARG 0.003 0.000 ARG R 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.612 Fit side-chains REVERT: R 406 GLU cc_start: 0.8531 (pm20) cc_final: 0.8169 (pm20) REVERT: H 19 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7471 (mtp85) REVERT: H 121 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.5711 (pm20) REVERT: N 58 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: N 169 GLU cc_start: 0.7535 (mp0) cc_final: 0.6992 (mp0) outliers start: 17 outliers final: 11 residues processed: 101 average time/residue: 0.1393 time to fit residues: 18.8732 Evaluate side-chains 103 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain N residue 58 PHE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 274 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 437 ASN R 498 GLN H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.174890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148636 restraints weight = 6576.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.152324 restraints weight = 8324.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.154427 restraints weight = 5030.912| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4749 Z= 0.244 Angle : 0.668 8.677 6444 Z= 0.341 Chirality : 0.045 0.191 697 Planarity : 0.006 0.067 819 Dihedral : 6.416 46.482 694 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.76 % Favored : 92.06 % Rotamer: Outliers : 3.19 % Allowed : 16.14 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -1.96 (0.36), residues: 554 helix: -2.72 (0.88), residues: 27 sheet: -0.25 (0.39), residues: 200 loop : -1.93 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 353 HIS 0.001 0.000 HIS H 59 PHE 0.024 0.002 PHE N 43 TYR 0.018 0.001 TYR H 102 ARG 0.003 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.570 Fit side-chains REVERT: R 406 GLU cc_start: 0.8611 (pm20) cc_final: 0.8238 (pm20) REVERT: R 438 SER cc_start: 0.7881 (p) cc_final: 0.7314 (p) REVERT: H 34 MET cc_start: 0.7608 (mmm) cc_final: 0.7391 (mmt) REVERT: H 121 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.5710 (pm20) REVERT: N 58 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: N 169 GLU cc_start: 0.7578 (mp0) cc_final: 0.6952 (mp0) outliers start: 16 outliers final: 12 residues processed: 98 average time/residue: 0.1381 time to fit residues: 18.1346 Evaluate side-chains 102 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 498 GLN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain N residue 58 PHE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 274 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 0.0050 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 498 GLN L 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.135325 restraints weight = 6515.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.137716 restraints weight = 10235.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.139391 restraints weight = 5853.565| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4749 Z= 0.227 Angle : 0.670 8.268 6444 Z= 0.340 Chirality : 0.045 0.190 697 Planarity : 0.006 0.067 819 Dihedral : 5.631 46.414 694 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.94 % Favored : 91.88 % Rotamer: Outliers : 3.19 % Allowed : 17.13 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -1.95 (0.36), residues: 554 helix: -2.67 (0.89), residues: 27 sheet: -0.26 (0.39), residues: 200 loop : -1.92 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 3 HIS 0.000 0.000 HIS N 66 PHE 0.024 0.002 PHE N 43 TYR 0.016 0.001 TYR H 95 ARG 0.003 0.000 ARG R 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.531 Fit side-chains REVERT: R 406 GLU cc_start: 0.8451 (pm20) cc_final: 0.8177 (pm20) REVERT: R 438 SER cc_start: 0.7980 (p) cc_final: 0.7415 (p) REVERT: H 121 GLN cc_start: 0.6594 (OUTLIER) cc_final: 0.5637 (pm20) REVERT: N 58 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: N 169 GLU cc_start: 0.7494 (mp0) cc_final: 0.6917 (mp0) outliers start: 16 outliers final: 11 residues processed: 97 average time/residue: 0.1518 time to fit residues: 19.3067 Evaluate side-chains 101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain N residue 58 PHE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 274 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.160890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137889 restraints weight = 6486.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140661 restraints weight = 9310.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140980 restraints weight = 4712.255| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4749 Z= 0.163 Angle : 0.630 8.044 6444 Z= 0.320 Chirality : 0.043 0.189 697 Planarity : 0.005 0.064 819 Dihedral : 5.048 44.286 694 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.76 % Favored : 92.06 % Rotamer: Outliers : 2.79 % Allowed : 18.53 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -1.88 (0.36), residues: 554 helix: -2.59 (0.91), residues: 27 sheet: -0.26 (0.39), residues: 201 loop : -1.84 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 3 HIS 0.001 0.000 HIS L 96 PHE 0.021 0.001 PHE N 43 TYR 0.012 0.001 TYR R 380 ARG 0.004 0.000 ARG R 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.47 seconds wall clock time: 33 minutes 11.12 seconds (1991.12 seconds total)