Starting phenix.real_space_refine on Tue Feb 11 08:19:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ey4_31377/02_2025/7ey4_31377.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ey4_31377/02_2025/7ey4_31377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ey4_31377/02_2025/7ey4_31377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ey4_31377/02_2025/7ey4_31377.map" model { file = "/net/cci-nas-00/data/ceres_data/7ey4_31377/02_2025/7ey4_31377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ey4_31377/02_2025/7ey4_31377.cif" } resolution = 3.69 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= 0.023 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 17 5.16 5 C 3000 2.51 5 N 772 2.21 5 O 894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4683 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 985 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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: "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: 4.38, per 1000 atoms: 0.94 Number of scatterers: 4683 At special positions: 0 Unit cell: (62.13, 80.66, 110.09, 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 17 16.00 O 894 8.00 N 772 7.00 C 3000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 166 " distance=2.05 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: 1.27 Conformation dependent library (CDL) restraints added in 553.9 milliseconds 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1072 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 11 sheets defined 7.2% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.648A pdb=" N ASP H 31 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.577A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 3.653A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.923A pdb=" N GLU L 70 " --> pdb=" O PHE L 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.193A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.513A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP H 73 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 47 removed outlier: 4.277A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG H 98 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 49 through 50 removed outlier: 3.668A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 356 through 358 removed outlier: 3.687A pdb=" N ILE R 402 " --> pdb=" O TYR R 508 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'N' and resid 50 through 55 removed outlier: 3.774A pdb=" N ASP N 53 " --> pdb=" O ARG N 273 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP N 287 " --> pdb=" O LYS N 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 63 through 64 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 63 through 64 current: chain 'N' and resid 116 through 121 removed outlier: 4.174A pdb=" N ASN N 164 " --> pdb=" O GLU N 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 163 through 164 current: chain 'N' and resid 200 through 205 removed outlier: 5.953A pdb=" N SER N 205 " --> pdb=" O PRO N 225 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 252 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: 1.27 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1473 1.35 - 1.48: 1418 1.48 - 1.61: 1891 1.61 - 1.74: 0 1.74 - 1.88: 21 Bond restraints: 4803 Sorted by residual: bond pdb=" CA SER H 107 " pdb=" CB SER H 107 " ideal model delta sigma weight residual 1.532 1.464 0.067 1.82e-02 3.02e+03 1.37e+01 bond pdb=" N CYS N 166 " pdb=" CA CYS N 166 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.58e+00 bond pdb=" N PHE N 168 " pdb=" CA PHE N 168 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.22e-02 6.72e+03 7.54e+00 bond pdb=" CA SER H 104 " pdb=" CB SER H 104 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.22e-02 6.72e+03 7.34e+00 bond pdb=" N ASP H 105 " pdb=" CA ASP H 105 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.34e-02 5.57e+03 7.04e+00 ... (remaining 4798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 6374 2.63 - 5.25: 127 5.25 - 7.88: 15 7.88 - 10.50: 1 10.50 - 13.13: 2 Bond angle restraints: 6519 Sorted by residual: angle pdb=" N VAL L 29 " pdb=" CA VAL L 29 " pdb=" C VAL L 29 " ideal model delta sigma weight residual 111.90 107.22 4.68 8.10e-01 1.52e+00 3.34e+01 angle pdb=" CA CYS R 379 " pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 114.40 127.53 -13.13 2.30e+00 1.89e-01 3.26e+01 angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 127.18 -12.78 2.30e+00 1.89e-01 3.09e+01 angle pdb=" N CYS R 379 " pdb=" CA CYS R 379 " pdb=" C CYS R 379 " ideal model delta sigma weight residual 108.38 114.13 -5.75 1.35e+00 5.49e-01 1.82e+01 angle pdb=" N CYS R 432 " pdb=" CA CYS R 432 " pdb=" C CYS R 432 " ideal model delta sigma weight residual 108.60 114.65 -6.05 1.46e+00 4.69e-01 1.71e+01 ... (remaining 6514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 2582 21.25 - 42.51: 184 42.51 - 63.76: 27 63.76 - 85.01: 13 85.01 - 106.26: 12 Dihedral angle restraints: 2818 sinusoidal: 1129 harmonic: 1689 Sorted by residual: 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 180.00 132.41 47.59 0 5.00e+00 4.00e-02 9.06e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual -86.00 -10.28 -75.72 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CA CYS R 379 " pdb=" C CYS R 379 " pdb=" N TYR R 380 " pdb=" CA TYR R 380 " ideal model delta harmonic sigma weight residual -180.00 -140.32 -39.68 0 5.00e+00 4.00e-02 6.30e+01 ... (remaining 2815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 624 0.078 - 0.156: 70 0.156 - 0.233: 4 0.233 - 0.311: 2 0.311 - 0.389: 1 Chirality restraints: 701 Sorted by residual: chirality pdb=" C1 BMA A 3 " pdb=" O4 NAG A 2 " pdb=" C2 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.79e+02 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.58e+00 chirality pdb=" CA CYS R 432 " pdb=" N CYS R 432 " pdb=" C CYS R 432 " pdb=" CB CYS R 432 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 698 not shown) Planarity restraints: 836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.322 2.00e-02 2.50e+03 2.72e-01 9.26e+02 pdb=" C7 NAG A 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.471 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.293 2.00e-02 2.50e+03 2.52e-01 7.94e+02 pdb=" C7 NAG A 2 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.007 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.430 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO L 8 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.035 5.00e-02 4.00e+02 ... (remaining 833 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 180 2.70 - 3.25: 4472 3.25 - 3.80: 6731 3.80 - 4.35: 8835 4.35 - 4.90: 15297 Nonbonded interactions: 35515 Sorted by model distance: nonbonded pdb=" OH TYR N 37 " pdb=" O LEU N 54 " model vdw 2.150 3.040 nonbonded pdb=" OD1 ASP N 40 " pdb=" OH TYR N 204 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR N 91 " pdb=" OE1 GLU N 191 " model vdw 2.217 3.040 nonbonded pdb=" NH2 ARG H 98 " pdb=" OD2 ASP H 117 " model vdw 2.237 3.120 nonbonded pdb=" NH2 ARG L 31 " pdb=" OE1 GLU R 340 " model vdw 2.241 3.120 ... (remaining 35510 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: 3.360 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.380 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.007 0.068 4803 Z= 0.449 Angle : 0.901 13.127 6519 Z= 0.512 Chirality : 0.053 0.389 701 Planarity : 0.014 0.272 835 Dihedral : 16.811 106.261 1728 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.50 % Favored : 86.15 % Rotamer: Outliers : 0.20 % Allowed : 0.60 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.36 % 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: -2.54 (0.34), residues: 563 helix: -3.57 (0.84), residues: 20 sheet: -0.83 (0.39), residues: 181 loop : -2.14 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 436 HIS 0.001 0.001 HIS N 66 PHE 0.028 0.002 PHE H 56 TYR 0.024 0.002 TYR H 110 ARG 0.017 0.001 ARG N 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.480 Fit side-chains REVERT: H 74 ASP cc_start: 0.8334 (m-30) cc_final: 0.7991 (m-30) REVERT: N 54 LEU cc_start: 0.7149 (mp) cc_final: 0.6142 (mt) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2320 time to fit residues: 35.0471 Evaluate side-chains 98 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 3.9990 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.0040 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 ASN N 164 ASN N 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.148078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117337 restraints weight = 6484.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119545 restraints weight = 4909.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121324 restraints weight = 4080.349| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4803 Z= 0.230 Angle : 0.726 8.089 6519 Z= 0.378 Chirality : 0.048 0.276 701 Planarity : 0.005 0.057 835 Dihedral : 12.746 85.147 708 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.41 % Favored : 90.41 % Rotamer: Outliers : 1.00 % Allowed : 11.40 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.14 (0.34), residues: 563 helix: -3.42 (0.95), residues: 20 sheet: -0.37 (0.39), residues: 192 loop : -2.01 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 436 HIS 0.000 0.000 HIS N 66 PHE 0.015 0.002 PHE N 43 TYR 0.015 0.001 TYR R 369 ARG 0.006 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.526 Fit side-chains REVERT: H 74 ASP cc_start: 0.8330 (m-30) cc_final: 0.8007 (m-30) REVERT: R 378 LYS cc_start: 0.7694 (ptpt) cc_final: 0.7486 (ptpp) REVERT: R 414 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7218 (mm-40) outliers start: 5 outliers final: 3 residues processed: 114 average time/residue: 0.2050 time to fit residues: 28.5717 Evaluate side-chains 92 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL 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 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 28 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117566 restraints weight = 6527.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119694 restraints weight = 5016.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121192 restraints weight = 4199.630| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4803 Z= 0.243 Angle : 0.702 8.142 6519 Z= 0.360 Chirality : 0.047 0.226 701 Planarity : 0.005 0.085 835 Dihedral : 10.444 75.002 708 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.59 % Favored : 90.23 % Rotamer: Outliers : 2.80 % Allowed : 15.00 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.03 (0.34), residues: 563 helix: -3.28 (0.98), residues: 20 sheet: -0.26 (0.39), residues: 186 loop : -1.94 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.014 0.002 PHE N 32 TYR 0.015 0.001 TYR H 110 ARG 0.005 0.001 ARG N 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.414 Fit side-chains REVERT: H 74 ASP cc_start: 0.8414 (m-30) cc_final: 0.8025 (m-30) outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.2141 time to fit residues: 27.0871 Evaluate side-chains 92 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114255 restraints weight = 6606.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116116 restraints weight = 5246.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117505 restraints weight = 4486.268| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4803 Z= 0.317 Angle : 0.720 8.071 6519 Z= 0.373 Chirality : 0.047 0.256 701 Planarity : 0.006 0.092 835 Dihedral : 8.836 60.510 708 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.41 % Favored : 90.41 % Rotamer: Outliers : 5.40 % Allowed : 15.60 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.02 (0.34), residues: 563 helix: -3.19 (0.93), residues: 20 sheet: -0.11 (0.40), residues: 185 loop : -2.02 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 436 HIS 0.002 0.001 HIS N 49 PHE 0.023 0.002 PHE H 56 TYR 0.013 0.001 TYR H 110 ARG 0.010 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: H 74 ASP cc_start: 0.8439 (m-30) cc_final: 0.8145 (m-30) REVERT: H 114 ASP cc_start: 0.9074 (t0) cc_final: 0.8846 (t0) REVERT: R 455 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9026 (tt) outliers start: 27 outliers final: 16 residues processed: 116 average time/residue: 0.2019 time to fit residues: 29.0766 Evaluate side-chains 106 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 455 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.141003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110483 restraints weight = 6583.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112663 restraints weight = 4990.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114258 restraints weight = 4149.876| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4803 Z= 0.319 Angle : 0.716 8.301 6519 Z= 0.370 Chirality : 0.047 0.227 701 Planarity : 0.005 0.085 835 Dihedral : 7.959 48.978 708 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 4.40 % Allowed : 17.40 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.35), residues: 563 helix: -3.07 (0.95), residues: 20 sheet: -0.12 (0.37), residues: 210 loop : -2.11 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 436 HIS 0.001 0.001 HIS N 66 PHE 0.020 0.002 PHE H 56 TYR 0.013 0.001 TYR H 110 ARG 0.010 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.605 Fit side-chains REVERT: L 81 GLU cc_start: 0.6344 (tp30) cc_final: 0.6015 (tp30) REVERT: H 74 ASP cc_start: 0.8439 (m-30) cc_final: 0.8162 (m-30) REVERT: H 114 ASP cc_start: 0.9102 (t0) cc_final: 0.8878 (t0) REVERT: N 52 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7594 (tm-30) outliers start: 22 outliers final: 16 residues processed: 118 average time/residue: 0.1878 time to fit residues: 27.4838 Evaluate side-chains 114 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 55 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.142825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112029 restraints weight = 6548.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114228 restraints weight = 4974.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115485 restraints weight = 4132.630| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4803 Z= 0.240 Angle : 0.737 18.347 6519 Z= 0.375 Chirality : 0.047 0.210 701 Planarity : 0.005 0.092 835 Dihedral : 6.995 39.992 708 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.60 % Allowed : 19.00 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.35), residues: 563 helix: -2.81 (1.01), residues: 20 sheet: -0.04 (0.38), residues: 200 loop : -1.95 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 436 HIS 0.001 0.000 HIS N 49 PHE 0.027 0.001 PHE N 43 TYR 0.010 0.001 TYR H 110 ARG 0.010 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.526 Fit side-chains REVERT: L 81 GLU cc_start: 0.6290 (tp30) cc_final: 0.5969 (tp30) REVERT: H 74 ASP cc_start: 0.8434 (m-30) cc_final: 0.8167 (m-30) REVERT: H 114 ASP cc_start: 0.9068 (t0) cc_final: 0.8850 (t0) REVERT: N 52 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7654 (pp30) outliers start: 18 outliers final: 12 residues processed: 112 average time/residue: 0.1883 time to fit residues: 26.1320 Evaluate side-chains 104 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 240 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111980 restraints weight = 6535.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114092 restraints weight = 5001.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115687 restraints weight = 4174.113| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4803 Z= 0.247 Angle : 0.727 17.963 6519 Z= 0.371 Chirality : 0.046 0.237 701 Planarity : 0.005 0.091 835 Dihedral : 6.308 38.900 708 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 3.60 % Allowed : 19.80 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.35), residues: 563 helix: -2.71 (1.05), residues: 20 sheet: 0.11 (0.38), residues: 196 loop : -1.87 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 436 HIS 0.001 0.000 HIS N 49 PHE 0.030 0.002 PHE N 43 TYR 0.011 0.001 TYR L 49 ARG 0.010 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.486 Fit side-chains REVERT: H 114 ASP cc_start: 0.9097 (t0) cc_final: 0.8845 (t0) REVERT: N 44 ARG cc_start: 0.5746 (ttm170) cc_final: 0.4698 (mpt180) REVERT: N 52 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7681 (pp30) outliers start: 18 outliers final: 15 residues processed: 101 average time/residue: 0.1933 time to fit residues: 24.0455 Evaluate side-chains 102 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111362 restraints weight = 6534.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113389 restraints weight = 5646.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114082 restraints weight = 4418.273| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4803 Z= 0.252 Angle : 0.721 16.794 6519 Z= 0.371 Chirality : 0.046 0.244 701 Planarity : 0.005 0.083 835 Dihedral : 5.895 37.827 708 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 3.80 % Allowed : 21.20 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.35), residues: 563 helix: -2.62 (1.07), residues: 20 sheet: 0.20 (0.39), residues: 190 loop : -1.91 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.033 0.002 PHE N 43 TYR 0.012 0.001 TYR H 110 ARG 0.013 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.540 Fit side-chains REVERT: H 114 ASP cc_start: 0.9078 (t0) cc_final: 0.8846 (t0) REVERT: R 493 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7928 (mm-40) REVERT: N 44 ARG cc_start: 0.6212 (ttm170) cc_final: 0.4835 (mpt180) REVERT: N 52 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7704 (pp30) outliers start: 19 outliers final: 15 residues processed: 109 average time/residue: 0.2094 time to fit residues: 27.8972 Evaluate side-chains 108 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.141766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111165 restraints weight = 6581.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112913 restraints weight = 5763.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113709 restraints weight = 4508.105| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4803 Z= 0.269 Angle : 0.726 15.819 6519 Z= 0.375 Chirality : 0.047 0.265 701 Planarity : 0.005 0.098 835 Dihedral : 5.794 39.309 708 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 3.20 % Allowed : 22.60 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.35), residues: 563 helix: -2.64 (1.06), residues: 20 sheet: 0.19 (0.37), residues: 200 loop : -2.01 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.032 0.002 PHE N 43 TYR 0.012 0.001 TYR H 110 ARG 0.011 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.508 Fit side-chains REVERT: H 114 ASP cc_start: 0.9071 (t0) cc_final: 0.8824 (t0) REVERT: R 493 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7974 (mm-40) REVERT: N 52 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7768 (pp30) outliers start: 16 outliers final: 16 residues processed: 98 average time/residue: 0.2078 time to fit residues: 24.9655 Evaluate side-chains 103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.0010 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.142705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111846 restraints weight = 6513.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113388 restraints weight = 5800.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113988 restraints weight = 4626.448| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4803 Z= 0.243 Angle : 0.717 15.026 6519 Z= 0.370 Chirality : 0.046 0.250 701 Planarity : 0.006 0.098 835 Dihedral : 5.661 37.469 708 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.20 % Allowed : 23.00 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.35), residues: 563 helix: -3.14 (0.84), residues: 26 sheet: 0.22 (0.39), residues: 190 loop : -1.82 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.032 0.002 PHE N 43 TYR 0.013 0.001 TYR H 110 ARG 0.012 0.001 ARG L 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.499 Fit side-chains REVERT: L 74 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8383 (p) REVERT: H 114 ASP cc_start: 0.9058 (t0) cc_final: 0.8827 (t0) REVERT: R 493 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7960 (mm-40) REVERT: N 52 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7784 (pp30) outliers start: 16 outliers final: 15 residues processed: 95 average time/residue: 0.1964 time to fit residues: 23.1005 Evaluate side-chains 103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 20 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.142178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112391 restraints weight = 6576.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113613 restraints weight = 5824.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114273 restraints weight = 4796.723| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4803 Z= 0.258 Angle : 0.719 14.598 6519 Z= 0.372 Chirality : 0.046 0.246 701 Planarity : 0.006 0.095 835 Dihedral : 5.651 38.463 708 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 3.20 % Allowed : 23.00 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.35), residues: 563 helix: -2.68 (1.05), residues: 20 sheet: 0.25 (0.39), residues: 190 loop : -1.91 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.031 0.002 PHE N 43 TYR 0.016 0.001 TYR H 110 ARG 0.012 0.001 ARG L 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.49 seconds wall clock time: 33 minutes 53.56 seconds (2033.56 seconds total)