Starting phenix.real_space_refine on Thu Mar 6 03:58:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eya_31380/03_2025/7eya_31380.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eya_31380/03_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_31380/03_2025/7eya_31380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eya_31380/03_2025/7eya_31380.map" model { file = "/net/cci-nas-00/data/ceres_data/7eya_31380/03_2025/7eya_31380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eya_31380/03_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-5624/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: 4.21, per 1000 atoms: 0.91 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: 1.13 Conformation dependent library (CDL) restraints added in 505.1 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: 0.54 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: 1.22 Time building geometry restraints manager: 1.35 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: 6.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.870 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.260 ------------------------------------------------------------------------------- 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 : 0.529 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: 0.1543 time to fit residues: 23.4442 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 : 0.568 ------------------------------------------------------------------------------- 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 = 0.140077 restraints weight = 9571.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141461 restraints weight = 6626.438| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 : 0.493 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: 0.1506 time to fit residues: 21.3120 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 : 0.528 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.3820 r_free = 0.3820 target = 0.160403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.137561 restraints weight = 6497.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.139570 restraints weight = 8895.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140607 restraints weight = 6763.574| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1787 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= 0.173 Angle : 0.634 8.962 6444 Z= 0.324 Chirality : 0.045 0.266 697 Planarity : 0.005 0.066 819 Dihedral : 10.415 76.103 694 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 1.00 % Allowed : 13.15 % Favored : 85.86 % 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: -2.70 (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 : 0.529 Fit side-chains REVERT: R 418 ILE cc_start: 0.9156 (tt) cc_final: 0.8935 (tt) REVERT: R 438 SER cc_start: 0.8068 (p) cc_final: 0.7680 (p) REVERT: L 25 MET cc_start: 0.6944 (mtp) cc_final: 0.6696 (mtp) REVERT: H 19 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7661 (mtp85) outliers start: 5 outliers final: 4 residues processed: 104 average time/residue: 0.1577 time to fit residues: 21.1239 Evaluate side-chains 98 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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: 0.6980 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.159360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138879 restraints weight = 6554.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141218 restraints weight = 10185.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.141510 restraints weight = 5288.268| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4749 Z= 0.205 Angle : 0.636 10.649 6444 Z= 0.324 Chirality : 0.045 0.267 697 Planarity : 0.005 0.068 819 Dihedral : 9.445 69.073 694 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.86 % Favored : 92.96 % Rotamer: Outliers : 1.59 % Allowed : 15.14 % Favored : 83.27 % 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: -1.99 (0.36), residues: 554 helix: -2.52 (1.15), residues: 19 sheet: -0.38 (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 0.035 0.002 PHE R 456 TYR 0.016 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 106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.543 Fit side-chains REVERT: R 355 ARG cc_start: 0.7810 (ttt90) cc_final: 0.7490 (ttt90) REVERT: R 418 ILE cc_start: 0.9171 (tt) cc_final: 0.8956 (tt) REVERT: R 438 SER cc_start: 0.8128 (p) cc_final: 0.7591 (p) REVERT: H 19 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7562 (mtp85) REVERT: N 169 GLU cc_start: 0.7472 (mp0) cc_final: 0.7002 (mp0) outliers start: 8 outliers final: 7 residues processed: 102 average time/residue: 0.1613 time to fit residues: 21.3382 Evaluate side-chains 101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.176553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149649 restraints weight = 6605.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153691 restraints weight = 7602.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.155710 restraints weight = 4654.448| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2222 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= 0.218 Angle : 0.639 8.695 6444 Z= 0.325 Chirality : 0.045 0.258 697 Planarity : 0.005 0.067 819 Dihedral : 8.828 62.916 694 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.58 % Favored : 92.24 % Rotamer: Outliers : 2.79 % Allowed : 15.94 % 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: -2.02 (0.36), residues: 554 helix: -2.38 (1.12), residues: 19 sheet: -0.35 (0.39), residues: 200 loop : -2.00 (0.33), residues: 335 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 0.024 0.001 PHE N 43 TYR 0.016 0.001 TYR H 95 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 105 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.493 Fit side-chains REVERT: R 355 ARG cc_start: 0.7820 (ttt90) cc_final: 0.7439 (ttt180) REVERT: R 438 SER cc_start: 0.7925 (p) cc_final: 0.7377 (p) REVERT: H 19 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7597 (mtp85) REVERT: N 58 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7439 (m-80) REVERT: N 169 GLU cc_start: 0.7538 (mp0) cc_final: 0.7055 (mp0) outliers start: 14 outliers final: 10 residues processed: 100 average time/residue: 0.1483 time to fit residues: 19.4527 Evaluate side-chains 101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 12 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.0470 chunk 30 optimal weight: 0.0770 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.177914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151171 restraints weight = 6552.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155614 restraints weight = 7582.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.157393 restraints weight = 4269.001| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2430 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= 0.178 Angle : 0.614 9.210 6444 Z= 0.312 Chirality : 0.044 0.248 697 Planarity : 0.005 0.067 819 Dihedral : 8.085 55.847 694 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.22 % Favored : 92.60 % Rotamer: Outliers : 3.19 % Allowed : 15.14 % 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: -1.96 (0.36), residues: 554 helix: -2.21 (1.15), residues: 19 sheet: -0.40 (0.39), residues: 205 loop : -1.92 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.001 0.000 HIS H 59 PHE 0.022 0.001 PHE N 43 TYR 0.013 0.001 TYR H 95 ARG 0.003 0.000 ARG H 100 *********************** 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 112 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.556 Fit side-chains REVERT: R 406 GLU cc_start: 0.8625 (pm20) cc_final: 0.8174 (pm20) REVERT: R 438 SER cc_start: 0.7922 (p) cc_final: 0.7362 (p) REVERT: L 25 MET cc_start: 0.7377 (mtp) cc_final: 0.7127 (mtp) REVERT: L 36 TYR cc_start: 0.8858 (m-80) cc_final: 0.8582 (m-80) REVERT: H 19 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7485 (mtp85) REVERT: H 121 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.5748 (pm20) REVERT: N 58 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: N 169 GLU cc_start: 0.7576 (mp0) cc_final: 0.7002 (mp0) outliers start: 16 outliers final: 11 residues processed: 104 average time/residue: 0.1499 time to fit residues: 20.6889 Evaluate side-chains 106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 121 GLN 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 Chi-restraints excluded: chain N residue 274 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 15 optimal weight: 0.0270 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 0.0170 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.160477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136736 restraints weight = 6577.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140025 restraints weight = 8822.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140651 restraints weight = 5177.181| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2507 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= 0.199 Angle : 0.623 9.400 6444 Z= 0.316 Chirality : 0.044 0.235 697 Planarity : 0.005 0.067 819 Dihedral : 7.624 50.206 694 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.22 % Favored : 92.60 % Rotamer: Outliers : 2.99 % Allowed : 15.54 % Favored : 81.47 % 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: -1.92 (0.36), residues: 554 helix: -1.00 (1.58), residues: 13 sheet: -0.41 (0.38), residues: 206 loop : -1.93 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 HIS 0.002 0.000 HIS H 59 PHE 0.024 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 107 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.491 Fit side-chains REVERT: R 406 GLU cc_start: 0.8464 (pm20) cc_final: 0.8182 (pm20) REVERT: R 438 SER cc_start: 0.7865 (p) cc_final: 0.7382 (p) REVERT: H 19 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7491 (mtp85) REVERT: H 121 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.5659 (pm20) REVERT: N 58 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: N 169 GLU cc_start: 0.7483 (mp0) cc_final: 0.6932 (mp0) outliers start: 15 outliers final: 13 residues processed: 100 average time/residue: 0.1427 time to fit residues: 18.8048 Evaluate side-chains 104 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 GLN 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 Chi-restraints excluded: chain N residue 274 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.0670 chunk 26 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 52 optimal weight: 0.3980 chunk 29 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.3096 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.161918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.138191 restraints weight = 6538.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.141531 restraints weight = 8847.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142189 restraints weight = 5070.079| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4749 Z= 0.151 Angle : 0.608 9.442 6444 Z= 0.308 Chirality : 0.043 0.221 697 Planarity : 0.005 0.066 819 Dihedral : 7.075 45.052 694 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.04 % Favored : 92.78 % Rotamer: Outliers : 2.59 % Allowed : 16.53 % Favored : 80.88 % 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: -1.81 (0.36), residues: 554 helix: -0.96 (1.59), residues: 13 sheet: -0.31 (0.38), residues: 205 loop : -1.88 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 436 HIS 0.001 0.000 HIS H 59 PHE 0.022 0.001 PHE N 43 TYR 0.012 0.001 TYR R 508 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 101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.482 Fit side-chains REVERT: R 406 GLU cc_start: 0.8538 (pm20) cc_final: 0.8167 (pm20) REVERT: L 36 TYR cc_start: 0.8835 (m-80) cc_final: 0.8569 (m-80) REVERT: H 19 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7474 (mtp85) REVERT: N 169 GLU cc_start: 0.7489 (mp0) cc_final: 0.6937 (mp0) outliers start: 13 outliers final: 10 residues processed: 95 average time/residue: 0.1373 time to fit residues: 17.5015 Evaluate side-chains 94 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 39 GLN 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 130 VAL Chi-restraints excluded: chain N residue 166 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.176173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.150304 restraints weight = 6600.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.154041 restraints weight = 8084.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.155552 restraints weight = 5040.633| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4749 Z= 0.225 Angle : 0.640 8.138 6444 Z= 0.328 Chirality : 0.044 0.187 697 Planarity : 0.006 0.079 819 Dihedral : 5.799 46.541 694 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.30 % Favored : 91.52 % Rotamer: Outliers : 3.19 % Allowed : 15.94 % Favored : 80.88 % 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: -2.08 (1.12), residues: 21 sheet: -0.23 (0.39), residues: 199 loop : -2.02 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 353 HIS 0.002 0.001 HIS H 59 PHE 0.026 0.002 PHE N 43 TYR 0.015 0.001 TYR H 95 ARG 0.004 0.000 ARG R 408 *********************** 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 104 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.547 Fit side-chains REVERT: R 406 GLU cc_start: 0.8547 (pm20) cc_final: 0.8308 (pm20) REVERT: R 438 SER cc_start: 0.7732 (p) cc_final: 0.7117 (p) REVERT: H 121 GLN cc_start: 0.6635 (OUTLIER) cc_final: 0.5691 (pm20) REVERT: N 58 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: N 169 GLU cc_start: 0.7564 (mp0) cc_final: 0.6959 (mp0) outliers start: 16 outliers final: 11 residues processed: 97 average time/residue: 0.1482 time to fit residues: 19.0667 Evaluate side-chains 100 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.160638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137725 restraints weight = 6499.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140848 restraints weight = 9166.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141799 restraints weight = 4533.699| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2759 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= 0.182 Angle : 0.610 7.943 6444 Z= 0.313 Chirality : 0.043 0.189 697 Planarity : 0.006 0.073 819 Dihedral : 5.053 45.400 694 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.40 % Favored : 92.42 % Rotamer: Outliers : 3.39 % Allowed : 16.14 % Favored : 80.48 % 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: -1.89 (0.37), residues: 554 helix: -2.68 (0.89), residues: 27 sheet: -0.22 (0.39), residues: 203 loop : -1.89 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.002 0.000 HIS H 59 PHE 0.022 0.001 PHE N 43 TYR 0.012 0.001 TYR H 95 ARG 0.007 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 106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.500 Fit side-chains REVERT: R 406 GLU cc_start: 0.8473 (pm20) cc_final: 0.8225 (pm20) REVERT: R 438 SER cc_start: 0.7878 (p) cc_final: 0.7284 (p) REVERT: R 508 TYR cc_start: 0.8445 (m-80) cc_final: 0.8222 (m-80) REVERT: H 121 GLN cc_start: 0.6614 (OUTLIER) cc_final: 0.5669 (pm20) REVERT: N 58 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: N 169 GLU cc_start: 0.7528 (mp0) cc_final: 0.6926 (mp0) outliers start: 17 outliers final: 13 residues processed: 98 average time/residue: 0.1441 time to fit residues: 18.6486 Evaluate side-chains 102 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 91 TYR 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 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.160788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136948 restraints weight = 6499.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140203 restraints weight = 9087.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141270 restraints weight = 5096.887| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4749 Z= 0.175 Angle : 0.607 7.999 6444 Z= 0.312 Chirality : 0.043 0.187 697 Planarity : 0.006 0.070 819 Dihedral : 5.016 45.259 694 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.58 % Favored : 92.24 % Rotamer: Outliers : 2.99 % Allowed : 16.14 % Favored : 80.88 % 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: -1.90 (0.36), residues: 554 helix: -2.64 (0.90), residues: 27 sheet: -0.21 (0.39), residues: 203 loop : -1.91 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 HIS 0.001 0.000 HIS H 59 PHE 0.023 0.001 PHE N 43 TYR 0.012 0.001 TYR H 95 ARG 0.007 0.000 ARG R 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1887.18 seconds wall clock time: 33 minutes 26.46 seconds (2006.46 seconds total)