Starting phenix.real_space_refine on Wed Mar 5 18:44:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6l_33643/03_2025/7y6l_33643.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6l_33643/03_2025/7y6l_33643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6l_33643/03_2025/7y6l_33643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6l_33643/03_2025/7y6l_33643.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6l_33643/03_2025/7y6l_33643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6l_33643/03_2025/7y6l_33643.cif" } resolution = 3.5 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= 0.008 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 16 5.16 5 C 2115 2.51 5 N 556 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 3308 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1519 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.71, per 1000 atoms: 0.82 Number of scatterers: 3308 At special positions: 0 Unit cell: (101.967, 72.952, 66.32, 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 16 16.00 O 621 8.00 N 556 7.00 C 2115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 360.1 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.5% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.140A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.722A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.063A pdb=" N LEU H 18 " --> pdb=" O TRP H 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.324A pdb=" N TRP H 33 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP H 57 " --> pdb=" O HIS H 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.795A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG H 98 " --> pdb=" O HIS H 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.450A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 113 hydrogen bonds defined for protein. 261 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1037 1.35 - 1.48: 969 1.48 - 1.60: 1371 1.60 - 1.73: 0 1.73 - 1.85: 20 Bond restraints: 3397 Sorted by residual: bond pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 1.808 1.850 -0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB VAL A 350 " pdb=" CG1 VAL A 350 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.34e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.34e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.63e-01 ... (remaining 3392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 4543 1.74 - 3.48: 67 3.48 - 5.22: 5 5.22 - 6.97: 2 6.97 - 8.71: 1 Bond angle restraints: 4618 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 123.11 -8.71 2.30e+00 1.89e-01 1.43e+01 angle pdb=" C LYS L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.11e+00 angle pdb=" C VAL A 350 " pdb=" CA VAL A 350 " pdb=" CB VAL A 350 " ideal model delta sigma weight residual 112.26 109.09 3.17 1.62e+00 3.81e-01 3.83e+00 angle pdb=" N VAL A 350 " pdb=" CA VAL A 350 " pdb=" C VAL A 350 " ideal model delta sigma weight residual 111.09 113.30 -2.21 1.25e+00 6.40e-01 3.14e+00 angle pdb=" CA TYR L 91 " pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 113.90 117.09 -3.19 1.80e+00 3.09e-01 3.13e+00 ... (remaining 4613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 1741 17.68 - 35.37: 211 35.37 - 53.05: 44 53.05 - 70.73: 8 70.73 - 88.42: 2 Dihedral angle restraints: 2006 sinusoidal: 785 harmonic: 1221 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 47.13 45.87 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 50.37 42.63 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -163.73 -16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 337 0.039 - 0.079: 113 0.079 - 0.118: 46 0.118 - 0.157: 2 0.157 - 0.197: 1 Chirality restraints: 499 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 496 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.034 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A 384 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 76 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C ILE H 76 " -0.022 2.00e-02 2.50e+03 pdb=" O ILE H 76 " 0.008 2.00e-02 2.50e+03 pdb=" N THR H 77 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 511 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" C VAL A 511 " -0.018 2.00e-02 2.50e+03 pdb=" O VAL A 511 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A 512 " 0.006 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 255 2.74 - 3.28: 3095 3.28 - 3.82: 5294 3.82 - 4.36: 6181 4.36 - 4.90: 11199 Nonbonded interactions: 26024 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.240 3.040 nonbonded pdb=" O SER A 443 " pdb=" NH1 ARG H 59 " model vdw 2.251 3.120 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.296 3.040 ... (remaining 26019 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.500 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 0.004 0.042 3397 Z= 0.231 Angle : 0.540 8.708 4618 Z= 0.286 Chirality : 0.045 0.197 499 Planarity : 0.004 0.052 586 Dihedral : 15.592 88.416 1214 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.56 % Allowed : 24.79 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.42), residues: 416 helix: -3.39 (0.77), residues: 27 sheet: 0.90 (0.45), residues: 153 loop : -0.53 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS H 110 PHE 0.011 0.001 PHE A 392 TYR 0.015 0.001 TYR L 91 ARG 0.004 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.344 Fit side-chains REVERT: A 357 ARG cc_start: 0.7266 (ttt-90) cc_final: 0.6858 (ttm-80) REVERT: A 403 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7560 (mtp180) REVERT: A 471 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6402 (mm-30) REVERT: H 17 SER cc_start: 0.8227 (m) cc_final: 0.7955 (p) REVERT: H 19 MET cc_start: 0.7052 (ttm) cc_final: 0.6608 (ttp) REVERT: H 21 SER cc_start: 0.7327 (p) cc_final: 0.7057 (t) REVERT: L 69 THR cc_start: 0.7509 (p) cc_final: 0.7144 (m) outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 0.1619 time to fit residues: 10.5151 Evaluate side-chains 39 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 105 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN H 67 HIS L 6 GLN L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.166503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.135608 restraints weight = 3546.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.137316 restraints weight = 2860.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.138783 restraints weight = 2498.910| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3397 Z= 0.167 Angle : 0.515 8.124 4618 Z= 0.273 Chirality : 0.045 0.199 499 Planarity : 0.004 0.041 586 Dihedral : 5.165 46.127 488 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.51 % Allowed : 22.54 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.42), residues: 416 helix: -2.76 (0.87), residues: 27 sheet: 1.02 (0.45), residues: 155 loop : -0.48 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.003 0.001 HIS H 110 PHE 0.007 0.001 PHE A 392 TYR 0.011 0.001 TYR L 91 ARG 0.003 0.000 ARG H 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.327 Fit side-chains REVERT: A 357 ARG cc_start: 0.7534 (ttt-90) cc_final: 0.7056 (ttm-80) REVERT: A 462 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6701 (mmtm) outliers start: 16 outliers final: 10 residues processed: 52 average time/residue: 0.1394 time to fit residues: 9.1851 Evaluate side-chains 42 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.160282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.129301 restraints weight = 3542.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.130914 restraints weight = 2905.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.131812 restraints weight = 2561.544| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 3397 Z= 0.384 Angle : 0.641 11.319 4618 Z= 0.337 Chirality : 0.050 0.219 499 Planarity : 0.005 0.040 586 Dihedral : 5.466 37.346 487 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 7.32 % Allowed : 21.69 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.41), residues: 416 helix: -2.87 (0.81), residues: 27 sheet: 0.81 (0.44), residues: 152 loop : -0.68 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 33 HIS 0.004 0.001 HIS H 110 PHE 0.016 0.002 PHE A 347 TYR 0.018 0.002 TYR L 91 ARG 0.003 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 36 time to evaluate : 0.359 Fit side-chains REVERT: A 357 ARG cc_start: 0.7583 (ttt-90) cc_final: 0.7184 (ttm-80) REVERT: A 390 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.5255 (tp) REVERT: A 454 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.7372 (ttm-80) REVERT: A 462 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6996 (mmtt) REVERT: H 10 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.5871 (mp0) REVERT: H 39 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7324 (tt0) outliers start: 26 outliers final: 18 residues processed: 58 average time/residue: 0.1418 time to fit residues: 10.4006 Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.163044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.132028 restraints weight = 3611.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.133677 restraints weight = 2938.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.134869 restraints weight = 2575.566| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3397 Z= 0.230 Angle : 0.559 10.357 4618 Z= 0.292 Chirality : 0.047 0.209 499 Planarity : 0.004 0.037 586 Dihedral : 5.081 36.750 486 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 7.32 % Allowed : 22.54 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.41), residues: 416 helix: -2.60 (0.87), residues: 27 sheet: 0.76 (0.44), residues: 152 loop : -0.62 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 33 HIS 0.002 0.001 HIS H 110 PHE 0.008 0.001 PHE A 347 TYR 0.013 0.001 TYR L 91 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 36 time to evaluate : 0.384 Fit side-chains REVERT: A 357 ARG cc_start: 0.7589 (ttt-90) cc_final: 0.7179 (ttm-80) REVERT: A 358 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.6230 (mp) REVERT: A 462 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6960 (mmtt) REVERT: H 10 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.5686 (mp0) outliers start: 26 outliers final: 17 residues processed: 61 average time/residue: 0.1453 time to fit residues: 11.1063 Evaluate side-chains 54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 34 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.160953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.129486 restraints weight = 3568.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.130861 restraints weight = 2945.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.132319 restraints weight = 2623.406| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 3397 Z= 0.314 Angle : 0.609 11.366 4618 Z= 0.316 Chirality : 0.049 0.278 499 Planarity : 0.004 0.036 586 Dihedral : 5.418 42.204 486 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 8.45 % Allowed : 21.69 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.41), residues: 416 helix: -1.96 (1.15), residues: 19 sheet: 0.64 (0.43), residues: 152 loop : -0.67 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 33 HIS 0.003 0.001 HIS H 110 PHE 0.011 0.002 PHE H 109 TYR 0.016 0.002 TYR A 369 ARG 0.007 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 36 time to evaluate : 0.361 Fit side-chains REVERT: A 357 ARG cc_start: 0.7644 (ttt-90) cc_final: 0.7214 (ttm-80) REVERT: A 462 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7025 (mmtt) REVERT: H 10 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.5740 (mp0) REVERT: H 39 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7316 (tt0) outliers start: 30 outliers final: 23 residues processed: 61 average time/residue: 0.1267 time to fit residues: 10.0211 Evaluate side-chains 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 32 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 103 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.166628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.135823 restraints weight = 3572.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.137583 restraints weight = 2906.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.138989 restraints weight = 2520.590| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3397 Z= 0.151 Angle : 0.526 9.720 4618 Z= 0.274 Chirality : 0.045 0.208 499 Planarity : 0.004 0.031 586 Dihedral : 5.118 43.696 486 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 6.48 % Allowed : 22.25 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.42), residues: 416 helix: -2.49 (0.91), residues: 27 sheet: 0.78 (0.43), residues: 151 loop : -0.55 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.001 0.000 HIS H 110 PHE 0.008 0.001 PHE A 515 TYR 0.010 0.001 TYR A 365 ARG 0.006 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 34 time to evaluate : 0.371 Fit side-chains REVERT: A 357 ARG cc_start: 0.7597 (ttt-90) cc_final: 0.7146 (ttm-80) REVERT: A 462 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6964 (mmtt) REVERT: H 10 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.5574 (mp0) outliers start: 23 outliers final: 20 residues processed: 54 average time/residue: 0.1337 time to fit residues: 9.2638 Evaluate side-chains 53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 31 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.0370 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.166405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.135881 restraints weight = 3509.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.137535 restraints weight = 2867.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.139064 restraints weight = 2507.046| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3397 Z= 0.174 Angle : 0.527 9.762 4618 Z= 0.275 Chirality : 0.045 0.212 499 Planarity : 0.004 0.030 586 Dihedral : 5.243 46.589 486 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 7.32 % Allowed : 21.97 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.42), residues: 416 helix: -2.14 (1.01), residues: 25 sheet: 0.89 (0.44), residues: 151 loop : -0.56 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.001 0.001 HIS H 110 PHE 0.007 0.001 PHE A 392 TYR 0.012 0.001 TYR A 369 ARG 0.005 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 34 time to evaluate : 0.334 Fit side-chains REVERT: A 357 ARG cc_start: 0.7600 (ttt-90) cc_final: 0.7150 (ttm-80) REVERT: A 358 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.6213 (mp) REVERT: A 462 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7023 (mmtt) REVERT: H 10 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.5722 (mp0) outliers start: 26 outliers final: 22 residues processed: 56 average time/residue: 0.1219 time to fit residues: 8.8786 Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 32 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 0.0020 chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.162402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.131374 restraints weight = 3528.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.132986 restraints weight = 2871.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.134406 restraints weight = 2532.857| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 3397 Z= 0.292 Angle : 0.605 11.026 4618 Z= 0.315 Chirality : 0.048 0.166 499 Planarity : 0.004 0.031 586 Dihedral : 5.807 49.717 486 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 8.17 % Allowed : 21.13 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.41), residues: 416 helix: -1.89 (1.14), residues: 19 sheet: 0.66 (0.43), residues: 153 loop : -0.54 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS H 67 PHE 0.009 0.002 PHE A 342 TYR 0.020 0.002 TYR L 91 ARG 0.004 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 34 time to evaluate : 0.343 Fit side-chains REVERT: A 357 ARG cc_start: 0.7604 (ttt-90) cc_final: 0.7163 (ttm-80) REVERT: A 358 ILE cc_start: 0.6528 (OUTLIER) cc_final: 0.6274 (mp) REVERT: A 462 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7059 (mmtt) REVERT: H 10 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.5740 (mp0) outliers start: 29 outliers final: 24 residues processed: 58 average time/residue: 0.1456 time to fit residues: 10.5868 Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 32 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.165794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.137672 restraints weight = 3522.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.135702 restraints weight = 2790.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.136997 restraints weight = 2896.136| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3397 Z= 0.170 Angle : 0.523 8.583 4618 Z= 0.278 Chirality : 0.046 0.209 499 Planarity : 0.004 0.030 586 Dihedral : 5.448 47.044 486 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 7.89 % Allowed : 20.85 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.42), residues: 416 helix: -2.23 (0.97), residues: 25 sheet: 0.79 (0.44), residues: 153 loop : -0.46 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 83 HIS 0.001 0.000 HIS H 110 PHE 0.007 0.001 PHE A 392 TYR 0.011 0.001 TYR L 91 ARG 0.007 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 35 time to evaluate : 0.322 Fit side-chains REVERT: A 357 ARG cc_start: 0.7609 (ttt-90) cc_final: 0.7178 (ttm-80) REVERT: A 358 ILE cc_start: 0.6526 (OUTLIER) cc_final: 0.6303 (mp) REVERT: A 462 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7015 (mmtt) REVERT: H 10 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.5645 (mp0) outliers start: 28 outliers final: 21 residues processed: 59 average time/residue: 0.1388 time to fit residues: 10.4752 Evaluate side-chains 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 34 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.166337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.135648 restraints weight = 3466.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.137267 restraints weight = 2794.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.138779 restraints weight = 2449.389| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3397 Z= 0.166 Angle : 0.521 8.326 4618 Z= 0.273 Chirality : 0.046 0.216 499 Planarity : 0.004 0.030 586 Dihedral : 5.223 43.725 486 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 6.76 % Allowed : 22.25 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.42), residues: 416 helix: -1.57 (1.20), residues: 19 sheet: 0.86 (0.44), residues: 153 loop : -0.27 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 33 HIS 0.001 0.001 HIS H 110 PHE 0.007 0.001 PHE A 392 TYR 0.012 0.001 TYR A 369 ARG 0.009 0.000 ARG A 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 33 time to evaluate : 0.369 Fit side-chains REVERT: A 357 ARG cc_start: 0.7604 (ttt-90) cc_final: 0.7146 (ttm-80) REVERT: A 358 ILE cc_start: 0.6461 (OUTLIER) cc_final: 0.6237 (mp) REVERT: A 462 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7059 (mmtt) REVERT: H 10 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.5644 (mp0) REVERT: H 97 THR cc_start: 0.9450 (m) cc_final: 0.9027 (p) outliers start: 24 outliers final: 20 residues processed: 54 average time/residue: 0.1396 time to fit residues: 9.9955 Evaluate side-chains 54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 31 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.163431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.132494 restraints weight = 3537.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.133941 restraints weight = 2891.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.135394 restraints weight = 2556.442| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3397 Z= 0.250 Angle : 0.568 9.415 4618 Z= 0.298 Chirality : 0.047 0.209 499 Planarity : 0.004 0.030 586 Dihedral : 5.606 44.048 486 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.76 % Allowed : 21.97 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.42), residues: 416 helix: -1.72 (1.15), residues: 19 sheet: 0.79 (0.43), residues: 153 loop : -0.36 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 33 HIS 0.002 0.001 HIS H 67 PHE 0.008 0.001 PHE A 374 TYR 0.018 0.002 TYR L 91 ARG 0.009 0.001 ARG A 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1441.15 seconds wall clock time: 25 minutes 38.03 seconds (1538.03 seconds total)