Starting phenix.real_space_refine on Thu Mar 6 04:10:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ey4_31377/03_2025/7ey4_31377.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ey4_31377/03_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_31377/03_2025/7ey4_31377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ey4_31377/03_2025/7ey4_31377.map" model { file = "/net/cci-nas-00/data/ceres_data/7ey4_31377/03_2025/7ey4_31377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ey4_31377/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 1.30 Conformation dependent library (CDL) restraints added in 518.0 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: 0.58 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: 1.18 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.170 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.640 ------------------------------------------------------------------------------- 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 : 0.526 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: 0.2217 time to fit residues: 33.5315 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 : 0.529 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117313 restraints weight = 6484.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119655 restraints weight = 4909.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121241 restraints weight = 4069.723| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.534 Fit side-chains REVERT: H 74 ASP cc_start: 0.8332 (m-30) cc_final: 0.8006 (m-30) REVERT: R 378 LYS cc_start: 0.7692 (ptpt) cc_final: 0.7484 (ptpp) REVERT: R 414 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7222 (mm-40) outliers start: 5 outliers final: 3 residues processed: 114 average time/residue: 0.2042 time to fit residues: 28.4810 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 : 0.524 ------------------------------------------------------------------------------- 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: 0.0270 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.148962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119275 restraints weight = 6506.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121362 restraints weight = 4986.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122768 restraints weight = 4155.826| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4803 Z= 0.217 Angle : 0.692 8.514 6519 Z= 0.354 Chirality : 0.047 0.229 701 Planarity : 0.005 0.088 835 Dihedral : 10.581 76.632 708 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.88 % Favored : 90.94 % Rotamer: Outliers : 2.40 % Allowed : 14.20 % Favored : 83.40 % 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: -1.98 (0.34), residues: 563 helix: -3.26 (1.00), residues: 20 sheet: -0.21 (0.39), residues: 186 loop : -1.91 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.012 0.001 PHE N 32 TYR 0.014 0.001 TYR R 369 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: 12 poor density : 96 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: H 74 ASP cc_start: 0.8385 (m-30) cc_final: 0.8034 (m-30) REVERT: R 414 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7236 (mm-40) REVERT: N 104 TRP cc_start: 0.8845 (m-90) cc_final: 0.8629 (m-90) outliers start: 12 outliers final: 9 residues processed: 103 average time/residue: 0.2051 time to fit residues: 25.6858 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 : 0.478 ------------------------------------------------------------------------------- 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: 0.0470 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.144742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114884 restraints weight = 6603.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116866 restraints weight = 5206.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118304 restraints weight = 4421.800| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2992 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= 0.307 Angle : 0.711 7.902 6519 Z= 0.368 Chirality : 0.047 0.249 701 Planarity : 0.006 0.091 835 Dihedral : 9.153 63.990 708 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.59 % Favored : 90.23 % Rotamer: Outliers : 5.40 % Allowed : 14.60 % Favored : 80.00 % 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: -1.99 (0.34), residues: 563 helix: -3.19 (0.93), residues: 20 sheet: -0.13 (0.39), residues: 185 loop : -1.98 (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 0.022 0.002 PHE H 56 TYR 0.013 0.002 TYR H 110 ARG 0.011 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 119 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.538 Fit side-chains REVERT: L 93 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7620 (m-40) REVERT: H 74 ASP cc_start: 0.8444 (m-30) cc_final: 0.8119 (m-30) REVERT: R 378 LYS cc_start: 0.7952 (ptpt) cc_final: 0.7751 (ptpp) outliers start: 27 outliers final: 17 residues processed: 111 average time/residue: 0.1994 time to fit residues: 27.1077 Evaluate side-chains 103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 56 THR 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 L residue 93 ASN Chi-restraints excluded: chain H residue 5 VAL 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 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: 0.9980 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.0170 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.146119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116202 restraints weight = 6576.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118060 restraints weight = 5157.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119493 restraints weight = 4378.798| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4803 Z= 0.242 Angle : 0.678 8.273 6519 Z= 0.349 Chirality : 0.046 0.238 701 Planarity : 0.005 0.082 835 Dihedral : 8.039 52.495 708 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 4.40 % Allowed : 16.60 % 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: -1.90 (0.35), residues: 563 helix: -2.98 (0.98), residues: 20 sheet: -0.04 (0.39), residues: 190 loop : -1.97 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 436 HIS 0.001 0.000 HIS N 66 PHE 0.013 0.002 PHE N 43 TYR 0.011 0.001 TYR H 110 ARG 0.012 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 120 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.499 Fit side-chains REVERT: L 93 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7634 (m-40) REVERT: H 74 ASP cc_start: 0.8468 (m-30) cc_final: 0.8166 (m-30) outliers start: 22 outliers final: 16 residues processed: 113 average time/residue: 0.1959 time to fit residues: 27.2963 Evaluate side-chains 105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 L residue 93 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain R residue 345 THR 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 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: 0.4980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 chunk 4 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.143504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112959 restraints weight = 6499.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115021 restraints weight = 4964.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116655 restraints weight = 4152.830| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4803 Z= 0.234 Angle : 0.681 8.092 6519 Z= 0.349 Chirality : 0.046 0.212 701 Planarity : 0.005 0.091 835 Dihedral : 7.113 41.124 708 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.00 % Allowed : 18.40 % Favored : 77.60 % 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: -1.84 (0.35), residues: 563 helix: -2.74 (1.03), residues: 20 sheet: 0.14 (0.38), residues: 201 loop : -2.10 (0.31), residues: 342 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 0.002 PHE N 168 TYR 0.010 0.001 TYR H 110 ARG 0.011 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 114 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.496 Fit side-chains outliers start: 20 outliers final: 15 residues processed: 106 average time/residue: 0.1919 time to fit residues: 25.1519 Evaluate side-chains 103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU 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 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.142029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111108 restraints weight = 6524.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113211 restraints weight = 5022.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114544 restraints weight = 4214.927| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3650 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= 0.275 Angle : 0.695 7.368 6519 Z= 0.361 Chirality : 0.046 0.177 701 Planarity : 0.005 0.090 835 Dihedral : 6.487 38.668 708 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 4.20 % Allowed : 19.20 % 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: -1.85 (0.34), residues: 563 helix: -2.76 (1.02), residues: 20 sheet: 0.10 (0.38), residues: 202 loop : -2.09 (0.31), residues: 341 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 0.026 0.002 PHE N 43 TYR 0.013 0.001 TYR H 110 ARG 0.011 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 117 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.546 Fit side-chains REVERT: N 44 ARG cc_start: 0.5737 (ttm170) cc_final: 0.4871 (mpt180) REVERT: N 52 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7652 (pp30) outliers start: 21 outliers final: 17 residues processed: 107 average time/residue: 0.2024 time to fit residues: 26.7817 Evaluate side-chains 107 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 L residue 103 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU 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 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: 0.0070 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.142135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111169 restraints weight = 6537.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113120 restraints weight = 5069.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114704 restraints weight = 4289.035| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4803 Z= 0.271 Angle : 0.760 21.179 6519 Z= 0.389 Chirality : 0.047 0.280 701 Planarity : 0.005 0.081 835 Dihedral : 6.059 38.468 708 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 3.80 % Allowed : 20.40 % Favored : 75.80 % 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: -1.77 (0.35), residues: 563 helix: -2.64 (1.06), residues: 20 sheet: 0.09 (0.38), residues: 200 loop : -1.98 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 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 0.012 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 112 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.531 Fit side-chains REVERT: N 44 ARG cc_start: 0.5808 (ttm170) cc_final: 0.4796 (mpt180) REVERT: N 52 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7687 (pp30) outliers start: 19 outliers final: 16 residues processed: 105 average time/residue: 0.1968 time to fit residues: 25.4607 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 : 0.530 ------------------------------------------------------------------------------- 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 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 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 130 VAL Chi-restraints excluded: chain N residue 240 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 40 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.144720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114144 restraints weight = 6528.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116186 restraints weight = 5144.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117646 restraints weight = 4357.862| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4803 Z= 0.210 Angle : 0.718 17.123 6519 Z= 0.371 Chirality : 0.046 0.298 701 Planarity : 0.005 0.082 835 Dihedral : 5.624 36.083 708 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.60 % Allowed : 21.60 % Favored : 74.80 % 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: -1.63 (0.35), residues: 563 helix: -2.57 (1.09), residues: 20 sheet: 0.28 (0.40), residues: 180 loop : -1.83 (0.31), residues: 363 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 0.030 0.001 PHE N 43 TYR 0.010 0.001 TYR H 110 ARG 0.012 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 110 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.510 Fit side-chains REVERT: L 74 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8370 (p) REVERT: R 493 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7889 (mm-40) REVERT: N 44 ARG cc_start: 0.5938 (ttm170) cc_final: 0.4809 (mpt180) REVERT: N 52 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7705 (pp30) outliers start: 18 outliers final: 15 residues processed: 102 average time/residue: 0.2020 time to fit residues: 25.3771 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 : 0.532 ------------------------------------------------------------------------------- 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 H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 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 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: 0.5980 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 15 optimal weight: 0.0050 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 29 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113886 restraints weight = 6444.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115935 restraints weight = 5001.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117551 restraints weight = 4215.932| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4803 Z= 0.211 Angle : 0.704 16.207 6519 Z= 0.363 Chirality : 0.046 0.263 701 Planarity : 0.005 0.097 835 Dihedral : 5.447 37.409 708 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.80 % Allowed : 21.40 % Favored : 74.80 % 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: -1.59 (0.35), residues: 563 helix: -3.12 (0.85), residues: 27 sheet: 0.25 (0.39), residues: 186 loop : -1.71 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 436 HIS 0.001 0.000 HIS N 49 PHE 0.032 0.001 PHE N 43 TYR 0.011 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 114 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.587 Fit side-chains REVERT: L 74 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8357 (p) REVERT: R 493 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7963 (mm-40) REVERT: N 44 ARG cc_start: 0.6020 (ttm170) cc_final: 0.4538 (mpt180) REVERT: N 52 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7737 (tm-30) outliers start: 19 outliers final: 18 residues processed: 104 average time/residue: 0.2230 time to fit residues: 28.3591 Evaluate side-chains 107 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 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 173 GLN 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: 0.2980 chunk 14 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.2338 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.146365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116411 restraints weight = 6486.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118513 restraints weight = 5533.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119618 restraints weight = 4436.094| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4803 Z= 0.196 Angle : 0.697 15.375 6519 Z= 0.357 Chirality : 0.045 0.250 701 Planarity : 0.006 0.097 835 Dihedral : 5.379 36.224 708 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 3.40 % Allowed : 22.20 % Favored : 74.40 % 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: -1.46 (0.35), residues: 563 helix: -3.09 (0.85), residues: 27 sheet: 0.34 (0.39), residues: 195 loop : -1.67 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 97 HIS 0.001 0.000 HIS N 49 PHE 0.030 0.001 PHE N 43 TYR 0.024 0.001 TYR R 421 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: 2646.30 seconds wall clock time: 47 minutes 30.65 seconds (2850.65 seconds total)