Starting phenix.real_space_refine on Thu Mar 6 04:12:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qic_13987/03_2025/7qic_13987.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qic_13987/03_2025/7qic_13987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qic_13987/03_2025/7qic_13987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qic_13987/03_2025/7qic_13987.map" model { file = "/net/cci-nas-00/data/ceres_data/7qic_13987/03_2025/7qic_13987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qic_13987/03_2025/7qic_13987.cif" } resolution = 4.1 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= 0.001 sd= 0.036 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 28 5.16 5 C 3148 2.51 5 N 809 2.21 5 O 855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 4841 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2991 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 12, 'TRANS': 388} Chain: "C" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.51, per 1000 atoms: 0.73 Number of scatterers: 4841 At special positions: 0 Unit cell: (88.536, 105.462, 76.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 Mg 1 11.99 O 855 8.00 N 809 7.00 C 3148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 638.7 milliseconds 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 55.4% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.519A pdb=" N THR A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 removed outlier: 3.666A pdb=" N LEU A 74 " --> pdb=" O PHE A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 75 through 99 removed outlier: 4.061A pdb=" N ILE A 79 " --> pdb=" O TRP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 111 through 144 removed outlier: 3.955A pdb=" N PHE A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 165 Processing helix chain 'A' and resid 169 through 179 Processing helix chain 'A' and resid 180 through 192 removed outlier: 4.103A pdb=" N THR A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.793A pdb=" N PHE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 277 removed outlier: 3.536A pdb=" N GLN A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.851A pdb=" N ARG A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 301 through 333 removed outlier: 3.641A pdb=" N PHE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.631A pdb=" N THR A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 345 removed outlier: 4.261A pdb=" N GLU A 345 " --> pdb=" O LYS A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 346 through 364 removed outlier: 3.570A pdb=" N LYS A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 removed outlier: 4.010A pdb=" N GLN A 379 " --> pdb=" O MET A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 399 removed outlier: 4.013A pdb=" N LEU A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 4.327A pdb=" N MET A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 437 Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.994A pdb=" N GLU B 111 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 108 through 112' Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.998A pdb=" N GLU C 23 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 68 " --> pdb=" O GLN C 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.816A pdb=" N ALA C 33 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 98 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.859A pdb=" N LEU B 18 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.510A pdb=" N ALA B 50 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 48 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY B 35 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B 97 " --> pdb=" O GLY B 35 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1530 1.34 - 1.46: 1163 1.46 - 1.58: 2201 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 4942 Sorted by residual: bond pdb=" CA TYR A 168 " pdb=" C TYR A 168 " ideal model delta sigma weight residual 1.523 1.537 -0.013 1.34e-02 5.57e+03 1.00e+00 bond pdb=" CA VAL A 205 " pdb=" CB VAL A 205 " ideal model delta sigma weight residual 1.526 1.540 -0.014 1.55e-02 4.16e+03 7.93e-01 bond pdb=" CA TYR A 168 " pdb=" CB TYR A 168 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 7.05e-01 bond pdb=" CA CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sigma weight residual 1.527 1.548 -0.020 2.48e-02 1.63e+03 6.73e-01 bond pdb=" N TYR A 168 " pdb=" CA TYR A 168 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.67e-01 ... (remaining 4937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 6534 1.66 - 3.32: 148 3.32 - 4.98: 28 4.98 - 6.64: 9 6.64 - 8.30: 2 Bond angle restraints: 6721 Sorted by residual: angle pdb=" N GLU B 89 " pdb=" CA GLU B 89 " pdb=" CB GLU B 89 " ideal model delta sigma weight residual 112.78 108.06 4.72 1.53e+00 4.27e-01 9.53e+00 angle pdb=" CA ASN C 83 " pdb=" C ASN C 83 " pdb=" O ASN C 83 " ideal model delta sigma weight residual 121.67 118.16 3.51 1.26e+00 6.30e-01 7.74e+00 angle pdb=" N ASN C 32 " pdb=" CA ASN C 32 " pdb=" C ASN C 32 " ideal model delta sigma weight residual 113.43 110.05 3.38 1.26e+00 6.30e-01 7.21e+00 angle pdb=" C THR A 130 " pdb=" N PHE A 131 " pdb=" CA PHE A 131 " ideal model delta sigma weight residual 120.72 116.25 4.47 1.67e+00 3.59e-01 7.18e+00 angle pdb=" CB MET A 89 " pdb=" CG MET A 89 " pdb=" SD MET A 89 " ideal model delta sigma weight residual 112.70 104.93 7.77 3.00e+00 1.11e-01 6.71e+00 ... (remaining 6716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 2615 15.91 - 31.82: 202 31.82 - 47.73: 61 47.73 - 63.64: 8 63.64 - 79.55: 3 Dihedral angle restraints: 2889 sinusoidal: 1068 harmonic: 1821 Sorted by residual: dihedral pdb=" CA GLN B 117 " pdb=" C GLN B 117 " pdb=" N GLY B 118 " pdb=" CA GLY B 118 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 124.62 -31.62 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" CA VAL C 28 " pdb=" C VAL C 28 " pdb=" N PHE C 29 " pdb=" CA PHE C 29 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 476 0.036 - 0.071: 238 0.071 - 0.106: 66 0.106 - 0.142: 13 0.142 - 0.177: 2 Chirality restraints: 795 Sorted by residual: chirality pdb=" CA PHE A 131 " pdb=" N PHE A 131 " pdb=" C PHE A 131 " pdb=" CB PHE A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB THR C 90 " pdb=" CA THR C 90 " pdb=" OG1 THR C 90 " pdb=" CG2 THR C 90 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA PRO A 228 " pdb=" N PRO A 228 " pdb=" C PRO A 228 " pdb=" CB PRO A 228 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 792 not shown) Planarity restraints: 837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 13 " 0.044 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO C 14 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 309 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C GLY A 309 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY A 309 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 310 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 131 " 0.014 2.00e-02 2.50e+03 1.30e-02 2.98e+00 pdb=" CG PHE A 131 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 131 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 131 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 131 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 131 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 131 " 0.001 2.00e-02 2.50e+03 ... (remaining 834 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 694 2.76 - 3.29: 4843 3.29 - 3.83: 7905 3.83 - 4.36: 8604 4.36 - 4.90: 15115 Nonbonded interactions: 37161 Sorted by model distance: nonbonded pdb=" O TYR B 94 " pdb=" OG1 THR B 119 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 103 " model vdw 2.269 3.040 nonbonded pdb=" O ASN A 126 " pdb=" OG1 THR A 130 " model vdw 2.296 3.040 nonbonded pdb=" O ARG B 52 " pdb=" NH1 ARG B 72 " model vdw 2.306 3.120 nonbonded pdb=" OG1 THR A 129 " pdb=" ND2 ASN A 382 " model vdw 2.341 3.120 ... (remaining 37156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.900 Find NCS groups from input model: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 : 0.003 0.034 4942 Z= 0.193 Angle : 0.650 8.303 6721 Z= 0.350 Chirality : 0.043 0.177 795 Planarity : 0.005 0.067 837 Dihedral : 12.831 79.553 1717 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.20 % Allowed : 0.40 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.34), residues: 633 helix: 0.77 (0.30), residues: 305 sheet: -1.57 (0.63), residues: 73 loop : -1.78 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 160 HIS 0.001 0.000 HIS A 207 PHE 0.030 0.001 PHE A 131 TYR 0.009 0.001 TYR A 185 ARG 0.009 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.468 Fit side-chains REVERT: A 120 LEU cc_start: 0.7446 (tt) cc_final: 0.7147 (mm) REVERT: A 182 PHE cc_start: 0.6387 (m-10) cc_final: 0.6106 (m-10) REVERT: A 246 LYS cc_start: 0.8682 (tttm) cc_final: 0.8177 (tptt) REVERT: C 14 PRO cc_start: 0.8515 (Cg_endo) cc_final: 0.8214 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.1555 time to fit residues: 29.0647 Evaluate side-chains 119 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.159104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130443 restraints weight = 7155.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130737 restraints weight = 6602.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.130917 restraints weight = 6901.574| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4942 Z= 0.226 Angle : 0.601 5.987 6721 Z= 0.319 Chirality : 0.044 0.184 795 Planarity : 0.005 0.052 837 Dihedral : 4.304 21.583 686 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.53 % Favored : 91.31 % Rotamer: Outliers : 0.40 % Allowed : 5.98 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.34), residues: 633 helix: 1.17 (0.29), residues: 316 sheet: -1.38 (0.65), residues: 73 loop : -1.88 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.001 0.001 HIS A 300 PHE 0.033 0.002 PHE A 131 TYR 0.014 0.001 TYR A 185 ARG 0.007 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.492 Fit side-chains REVERT: A 80 MET cc_start: 0.8651 (mmp) cc_final: 0.8301 (mmt) REVERT: A 142 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7288 (tm-30) REVERT: A 143 MET cc_start: 0.8635 (tpp) cc_final: 0.8234 (tpp) REVERT: A 246 LYS cc_start: 0.8802 (tttm) cc_final: 0.8272 (tptt) REVERT: A 319 CYS cc_start: 0.8116 (m) cc_final: 0.7849 (t) REVERT: C 47 LEU cc_start: 0.8406 (tp) cc_final: 0.8106 (tp) REVERT: B 37 PHE cc_start: 0.8489 (m-80) cc_final: 0.8260 (m-80) REVERT: B 47 PHE cc_start: 0.8668 (t80) cc_final: 0.8398 (t80) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.1536 time to fit residues: 27.9921 Evaluate side-chains 117 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.0670 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 58 optimal weight: 0.0170 chunk 57 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.3770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 382 ASN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.157583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.138231 restraints weight = 6490.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.139148 restraints weight = 5403.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.140022 restraints weight = 4781.869| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4942 Z= 0.179 Angle : 0.577 5.887 6721 Z= 0.307 Chirality : 0.043 0.190 795 Planarity : 0.004 0.054 837 Dihedral : 4.301 21.798 686 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.74 % Favored : 92.10 % Rotamer: Outliers : 0.20 % Allowed : 2.99 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.34), residues: 633 helix: 1.25 (0.29), residues: 316 sheet: -1.43 (0.63), residues: 73 loop : -1.91 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 53 HIS 0.001 0.001 HIS A 207 PHE 0.015 0.001 PHE C 50 TYR 0.009 0.001 TYR C 93 ARG 0.004 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.8790 (mmp) cc_final: 0.8314 (mmt) REVERT: A 246 LYS cc_start: 0.8523 (tttm) cc_final: 0.8183 (tptt) REVERT: A 252 LYS cc_start: 0.7873 (tptm) cc_final: 0.7347 (ttpt) REVERT: C 14 PRO cc_start: 0.8607 (Cg_exo) cc_final: 0.8372 (Cg_endo) REVERT: C 47 LEU cc_start: 0.8378 (tp) cc_final: 0.8099 (tp) REVERT: B 47 PHE cc_start: 0.8534 (t80) cc_final: 0.8312 (t80) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1490 time to fit residues: 26.6783 Evaluate side-chains 121 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.0570 chunk 1 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.157263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.137883 restraints weight = 6534.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.138784 restraints weight = 5418.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.139702 restraints weight = 4795.993| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4942 Z= 0.194 Angle : 0.574 5.745 6721 Z= 0.302 Chirality : 0.043 0.175 795 Planarity : 0.004 0.055 837 Dihedral : 4.244 22.106 686 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.20 % Allowed : 2.59 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.34), residues: 633 helix: 1.41 (0.29), residues: 310 sheet: -1.70 (0.58), residues: 84 loop : -1.81 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.001 0.001 HIS A 300 PHE 0.018 0.001 PHE A 131 TYR 0.012 0.001 TYR A 185 ARG 0.005 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: C 14 PRO cc_start: 0.8783 (Cg_exo) cc_final: 0.8173 (Cg_endo) REVERT: C 39 GLN cc_start: 0.6585 (tp-100) cc_final: 0.6384 (tp-100) REVERT: C 47 LEU cc_start: 0.8376 (tp) cc_final: 0.8144 (tp) REVERT: B 47 PHE cc_start: 0.8569 (t80) cc_final: 0.8299 (t80) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1376 time to fit residues: 25.1377 Evaluate side-chains 118 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN C 32 ASN C 58 ASN C 73 ASN C 76 ASN B 31 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.154071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.134731 restraints weight = 6658.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.134812 restraints weight = 7922.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.135154 restraints weight = 7407.859| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4942 Z= 0.231 Angle : 0.595 5.650 6721 Z= 0.313 Chirality : 0.043 0.177 795 Planarity : 0.004 0.056 837 Dihedral : 4.317 22.003 686 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.20 % Allowed : 2.79 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.34), residues: 633 helix: 1.40 (0.29), residues: 312 sheet: -1.59 (0.59), residues: 84 loop : -1.91 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.001 0.001 HIS A 300 PHE 0.023 0.001 PHE A 131 TYR 0.010 0.001 TYR A 185 ARG 0.005 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8408 (tttp) cc_final: 0.8166 (tptt) REVERT: A 252 LYS cc_start: 0.7997 (tptm) cc_final: 0.7527 (ttpt) REVERT: C 14 PRO cc_start: 0.8815 (Cg_exo) cc_final: 0.8197 (Cg_endo) REVERT: C 39 GLN cc_start: 0.6498 (tp-100) cc_final: 0.6259 (tp-100) REVERT: B 47 PHE cc_start: 0.8594 (t80) cc_final: 0.8249 (t80) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1286 time to fit residues: 23.6388 Evaluate side-chains 113 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 16 optimal weight: 0.0020 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 0.0070 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 32 ASN C 73 ASN C 76 ASN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.161957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.134290 restraints weight = 7209.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.133771 restraints weight = 6189.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.134246 restraints weight = 6281.333| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4942 Z= 0.175 Angle : 0.579 6.387 6721 Z= 0.300 Chirality : 0.042 0.170 795 Planarity : 0.005 0.074 837 Dihedral : 4.211 21.759 686 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.20 % Allowed : 2.39 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.34), residues: 633 helix: 1.52 (0.29), residues: 313 sheet: -1.54 (0.60), residues: 84 loop : -1.91 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 53 HIS 0.010 0.002 HIS B 31 PHE 0.023 0.001 PHE A 131 TYR 0.008 0.001 TYR A 185 ARG 0.006 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.525 Fit side-chains REVERT: A 51 MET cc_start: 0.7353 (tmm) cc_final: 0.7026 (tmm) REVERT: A 89 MET cc_start: 0.7746 (tpt) cc_final: 0.7402 (ttp) REVERT: A 246 LYS cc_start: 0.8685 (tttp) cc_final: 0.8284 (tptt) REVERT: A 252 LYS cc_start: 0.7924 (tptm) cc_final: 0.7608 (ttpt) REVERT: C 14 PRO cc_start: 0.8821 (Cg_exo) cc_final: 0.8289 (Cg_endo) REVERT: C 39 GLN cc_start: 0.6658 (tp-100) cc_final: 0.6431 (tp-100) REVERT: C 58 ASN cc_start: 0.8663 (p0) cc_final: 0.8305 (p0) REVERT: B 47 PHE cc_start: 0.8617 (t80) cc_final: 0.8306 (t80) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.1455 time to fit residues: 27.6871 Evaluate side-chains 117 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 11 optimal weight: 0.0670 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 44 optimal weight: 0.0570 overall best weight: 0.1034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN C 32 ASN C 73 ASN C 76 ASN B 31 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.167054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.139656 restraints weight = 7037.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.139555 restraints weight = 6110.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.140007 restraints weight = 6250.530| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4942 Z= 0.163 Angle : 0.612 7.606 6721 Z= 0.307 Chirality : 0.042 0.184 795 Planarity : 0.005 0.058 837 Dihedral : 4.124 21.113 686 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.20 % Allowed : 1.59 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.34), residues: 633 helix: 1.63 (0.29), residues: 316 sheet: -1.43 (0.61), residues: 79 loop : -1.92 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 160 HIS 0.004 0.001 HIS B 31 PHE 0.017 0.001 PHE A 327 TYR 0.009 0.001 TYR A 185 ARG 0.002 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.528 Fit side-chains REVERT: A 89 MET cc_start: 0.7764 (tpt) cc_final: 0.7512 (ttp) REVERT: A 385 ILE cc_start: 0.8121 (tp) cc_final: 0.7769 (tp) REVERT: C 14 PRO cc_start: 0.8823 (Cg_exo) cc_final: 0.8282 (Cg_endo) REVERT: C 30 MET cc_start: 0.6912 (ptm) cc_final: 0.6575 (ptm) REVERT: C 39 GLN cc_start: 0.6566 (tp-100) cc_final: 0.6344 (tp-100) REVERT: C 47 LEU cc_start: 0.8665 (tt) cc_final: 0.8385 (tp) REVERT: C 58 ASN cc_start: 0.8386 (p0) cc_final: 0.7988 (p0) REVERT: C 79 TYR cc_start: 0.8612 (m-80) cc_final: 0.8385 (m-10) REVERT: B 47 PHE cc_start: 0.8503 (t80) cc_final: 0.8245 (t80) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.1301 time to fit residues: 25.4481 Evaluate side-chains 123 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 16 optimal weight: 0.0030 chunk 40 optimal weight: 0.0670 chunk 53 optimal weight: 0.0070 chunk 11 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 0.0570 chunk 51 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN C 32 ASN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.169645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.142771 restraints weight = 7012.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.142507 restraints weight = 6275.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.143119 restraints weight = 6825.488| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4942 Z= 0.162 Angle : 0.581 7.419 6721 Z= 0.298 Chirality : 0.042 0.170 795 Planarity : 0.005 0.059 837 Dihedral : 4.123 21.082 686 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.35), residues: 633 helix: 1.68 (0.29), residues: 315 sheet: -1.42 (0.62), residues: 79 loop : -1.85 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 PHE 0.014 0.001 PHE C 50 TYR 0.018 0.001 TYR A 185 ARG 0.008 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.477 Fit side-chains REVERT: A 89 MET cc_start: 0.7728 (tpt) cc_final: 0.7522 (ttp) REVERT: A 249 PHE cc_start: 0.7296 (t80) cc_final: 0.6954 (t80) REVERT: A 385 ILE cc_start: 0.8025 (tp) cc_final: 0.7665 (tp) REVERT: C 14 PRO cc_start: 0.8817 (Cg_exo) cc_final: 0.8347 (Cg_endo) REVERT: C 58 ASN cc_start: 0.8034 (p0) cc_final: 0.7514 (p0) REVERT: C 79 TYR cc_start: 0.8586 (m-80) cc_final: 0.8340 (m-10) REVERT: B 47 PHE cc_start: 0.8531 (t80) cc_final: 0.8182 (t80) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1204 time to fit residues: 22.8869 Evaluate side-chains 120 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.163797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.137073 restraints weight = 6948.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.135041 restraints weight = 6918.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.137151 restraints weight = 7373.044| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4942 Z= 0.218 Angle : 0.614 8.226 6721 Z= 0.319 Chirality : 0.043 0.179 795 Planarity : 0.005 0.060 837 Dihedral : 4.148 21.282 686 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.20 % Allowed : 1.20 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.35), residues: 633 helix: 1.70 (0.29), residues: 315 sheet: -1.55 (0.61), residues: 84 loop : -1.86 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 53 HIS 0.002 0.001 HIS B 31 PHE 0.016 0.001 PHE C 50 TYR 0.008 0.001 TYR A 185 ARG 0.008 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.480 Fit side-chains REVERT: A 385 ILE cc_start: 0.7854 (tp) cc_final: 0.7582 (tp) REVERT: C 14 PRO cc_start: 0.8765 (Cg_exo) cc_final: 0.8346 (Cg_endo) REVERT: C 58 ASN cc_start: 0.8698 (p0) cc_final: 0.8300 (p0) REVERT: B 47 PHE cc_start: 0.8635 (t80) cc_final: 0.8246 (t80) outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.1217 time to fit residues: 23.4924 Evaluate side-chains 122 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 0.0040 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 0.0470 chunk 33 optimal weight: 0.0050 overall best weight: 0.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN C 32 ASN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.161690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.142468 restraints weight = 6465.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.143463 restraints weight = 5384.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.144291 restraints weight = 4749.776| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4942 Z= 0.170 Angle : 0.600 7.164 6721 Z= 0.309 Chirality : 0.043 0.177 795 Planarity : 0.005 0.062 837 Dihedral : 4.122 20.882 686 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.35), residues: 633 helix: 1.72 (0.29), residues: 315 sheet: -1.47 (0.61), residues: 84 loop : -1.74 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.001 0.000 HIS B 31 PHE 0.017 0.001 PHE C 50 TYR 0.020 0.001 TYR A 185 ARG 0.008 0.000 ARG C 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 385 ILE cc_start: 0.7616 (tp) cc_final: 0.7378 (tp) REVERT: C 14 PRO cc_start: 0.8801 (Cg_exo) cc_final: 0.8437 (Cg_endo) REVERT: C 30 MET cc_start: 0.8233 (pmm) cc_final: 0.6521 (ptm) REVERT: C 58 ASN cc_start: 0.8438 (p0) cc_final: 0.8022 (p0) REVERT: B 47 PHE cc_start: 0.8518 (t80) cc_final: 0.8180 (t80) REVERT: B 106 PHE cc_start: 0.7817 (m-10) cc_final: 0.7502 (m-10) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1552 time to fit residues: 29.3564 Evaluate side-chains 123 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 8 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.157144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.136925 restraints weight = 6647.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.137793 restraints weight = 5633.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.137838 restraints weight = 5022.581| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4942 Z= 0.232 Angle : 0.628 6.902 6721 Z= 0.326 Chirality : 0.044 0.176 795 Planarity : 0.005 0.061 837 Dihedral : 4.179 20.990 686 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.35), residues: 633 helix: 1.56 (0.29), residues: 320 sheet: -1.56 (0.61), residues: 84 loop : -1.78 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 53 HIS 0.002 0.001 HIS B 31 PHE 0.017 0.002 PHE C 50 TYR 0.012 0.001 TYR A 185 ARG 0.008 0.000 ARG C 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.93 seconds wall clock time: 35 minutes 43.04 seconds (2143.04 seconds total)