Starting phenix.real_space_refine on Fri Dec 27 12:43:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qic_13987/12_2024/7qic_13987.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qic_13987/12_2024/7qic_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_13987/12_2024/7qic_13987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qic_13987/12_2024/7qic_13987.map" model { file = "/net/cci-nas-00/data/ceres_data/7qic_13987/12_2024/7qic_13987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qic_13987/12_2024/7qic_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-5532/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: 3.46, per 1000 atoms: 0.71 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: 1.38 Conformation dependent library (CDL) restraints added in 666.3 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: 0.54 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: 1.27 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.090 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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: 0.010 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: 19.810 ------------------------------------------------------------------------------- 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 : 0.537 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: 0.1603 time to fit residues: 29.7867 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 : 0.527 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4942 Z= 0.225 Angle : 0.601 5.989 6721 Z= 0.318 Chirality : 0.044 0.184 795 Planarity : 0.005 0.052 837 Dihedral : 4.305 21.560 686 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.69 % Favored : 91.15 % 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: -1.39 (0.65), residues: 73 loop : -1.89 (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 0.006 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 : 0.606 Fit side-chains REVERT: A 80 MET cc_start: 0.8699 (mmp) cc_final: 0.8343 (mmt) REVERT: A 142 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 143 MET cc_start: 0.8656 (tpp) cc_final: 0.8244 (tpp) REVERT: A 191 MET cc_start: 0.6867 (ttp) cc_final: 0.6648 (ttp) REVERT: A 246 LYS cc_start: 0.8700 (tttm) cc_final: 0.8232 (tptt) REVERT: A 319 CYS cc_start: 0.8092 (m) cc_final: 0.7829 (t) REVERT: C 47 LEU cc_start: 0.8442 (tp) cc_final: 0.8123 (tp) REVERT: B 37 PHE cc_start: 0.8426 (m-80) cc_final: 0.8204 (m-80) REVERT: B 47 PHE cc_start: 0.8620 (t80) cc_final: 0.8366 (t80) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.1681 time to fit residues: 30.5909 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 : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 57 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1652 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= 0.193 Angle : 0.582 5.965 6721 Z= 0.309 Chirality : 0.043 0.188 795 Planarity : 0.004 0.054 837 Dihedral : 4.312 21.887 686 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.06 % Favored : 91.79 % 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: -0.39 (0.34), residues: 633 helix: 1.23 (0.29), residues: 316 sheet: -1.42 (0.64), residues: 73 loop : -1.91 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.001 0.001 HIS A 207 PHE 0.016 0.001 PHE C 50 TYR 0.010 0.001 TYR A 185 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 139 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.8795 (mmp) cc_final: 0.8302 (mmt) REVERT: A 246 LYS cc_start: 0.8737 (tttm) cc_final: 0.8258 (tptt) REVERT: A 252 LYS cc_start: 0.7947 (tptm) cc_final: 0.7300 (ttpt) REVERT: A 319 CYS cc_start: 0.8370 (m) cc_final: 0.8116 (t) REVERT: C 47 LEU cc_start: 0.8380 (tp) cc_final: 0.8105 (tp) REVERT: B 47 PHE cc_start: 0.8627 (t80) cc_final: 0.8371 (t80) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1679 time to fit residues: 30.1920 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 : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4942 Z= 0.250 Angle : 0.605 5.853 6721 Z= 0.318 Chirality : 0.044 0.184 795 Planarity : 0.004 0.055 837 Dihedral : 4.341 22.348 686 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.53 % Favored : 91.31 % Rotamer: Outliers : 0.20 % Allowed : 3.39 % Favored : 96.41 % 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: -0.37 (0.34), residues: 633 helix: 1.32 (0.29), residues: 310 sheet: -1.70 (0.58), residues: 84 loop : -1.80 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 53 HIS 0.001 0.001 HIS A 300 PHE 0.018 0.001 PHE A 131 TYR 0.014 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 137 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.8726 (mmp) cc_final: 0.8228 (mmt) REVERT: A 246 LYS cc_start: 0.8757 (tttm) cc_final: 0.8197 (tptt) REVERT: A 319 CYS cc_start: 0.8455 (m) cc_final: 0.8114 (t) REVERT: C 14 PRO cc_start: 0.8750 (Cg_endo) cc_final: 0.8437 (Cg_exo) REVERT: C 39 GLN cc_start: 0.6763 (tp-100) cc_final: 0.6543 (tp-100) REVERT: B 47 PHE cc_start: 0.8728 (t80) cc_final: 0.8341 (t80) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.1470 time to fit residues: 26.3368 Evaluate side-chains 116 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 C 73 ASN C 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1973 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= 0.222 Angle : 0.594 5.657 6721 Z= 0.313 Chirality : 0.043 0.178 795 Planarity : 0.004 0.057 837 Dihedral : 4.368 22.079 686 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.11 % Favored : 92.73 % Rotamer: Outliers : 0.20 % Allowed : 3.19 % Favored : 96.61 % 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: -0.36 (0.34), residues: 633 helix: 1.33 (0.29), residues: 312 sheet: -1.63 (0.59), residues: 84 loop : -1.84 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 53 HIS 0.001 0.001 HIS A 207 PHE 0.021 0.001 PHE A 131 TYR 0.011 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 135 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.539 Fit side-chains REVERT: A 80 MET cc_start: 0.8809 (mmp) cc_final: 0.8188 (mmt) REVERT: A 89 MET cc_start: 0.7715 (tpt) cc_final: 0.7505 (ttp) REVERT: A 107 ARG cc_start: 0.7713 (tpp80) cc_final: 0.7121 (ttt180) REVERT: A 246 LYS cc_start: 0.8713 (tttm) cc_final: 0.8237 (tptt) REVERT: A 319 CYS cc_start: 0.8476 (m) cc_final: 0.8122 (t) REVERT: C 47 LEU cc_start: 0.8531 (tp) cc_final: 0.8326 (tp) REVERT: B 47 PHE cc_start: 0.8677 (t80) cc_final: 0.8266 (t80) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1654 time to fit residues: 28.5974 Evaluate side-chains 115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 0.0270 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 32 ASN C 58 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2157 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= 0.199 Angle : 0.607 6.501 6721 Z= 0.313 Chirality : 0.043 0.173 795 Planarity : 0.005 0.072 837 Dihedral : 4.340 21.972 686 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.58 % Favored : 92.26 % 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: -0.28 (0.34), residues: 633 helix: 1.41 (0.29), residues: 311 sheet: -1.55 (0.60), residues: 84 loop : -1.83 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 53 HIS 0.001 0.001 HIS A 207 PHE 0.024 0.002 PHE A 327 TYR 0.009 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 137 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.7359 (tmm) cc_final: 0.7097 (tmm) REVERT: A 246 LYS cc_start: 0.8717 (tttm) cc_final: 0.8197 (tptt) REVERT: A 319 CYS cc_start: 0.8465 (m) cc_final: 0.8131 (t) REVERT: C 30 MET cc_start: 0.6959 (ptm) cc_final: 0.6717 (ptm) REVERT: C 39 GLN cc_start: 0.6589 (tp-100) cc_final: 0.6341 (tp-100) REVERT: B 47 PHE cc_start: 0.8589 (t80) cc_final: 0.8248 (t80) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.1400 time to fit residues: 25.5915 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 : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 0.0050 chunk 51 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2333 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= 0.183 Angle : 0.610 9.999 6721 Z= 0.310 Chirality : 0.043 0.173 795 Planarity : 0.005 0.058 837 Dihedral : 4.263 21.503 686 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % 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: -0.14 (0.34), residues: 633 helix: 1.53 (0.29), residues: 316 sheet: -1.49 (0.60), residues: 84 loop : -1.85 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 PHE 0.024 0.001 PHE A 131 TYR 0.009 0.001 TYR A 185 ARG 0.001 0.000 ARG B 72 *********************** 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 137 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.630 Fit side-chains REVERT: A 246 LYS cc_start: 0.8717 (tttm) cc_final: 0.8226 (tptt) REVERT: A 319 CYS cc_start: 0.8447 (m) cc_final: 0.8096 (t) REVERT: C 30 MET cc_start: 0.6888 (ptm) cc_final: 0.6633 (ptm) REVERT: C 47 LEU cc_start: 0.8597 (tt) cc_final: 0.8272 (tp) REVERT: C 58 ASN cc_start: 0.8604 (p0) cc_final: 0.8247 (p0) REVERT: B 47 PHE cc_start: 0.8631 (t80) cc_final: 0.8330 (t80) outliers start: 1 outliers final: 1 residues processed: 137 average time/residue: 0.1426 time to fit residues: 26.6993 Evaluate side-chains 115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.0670 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 C 73 ASN C 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2479 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= 0.180 Angle : 0.612 9.588 6721 Z= 0.312 Chirality : 0.043 0.191 795 Planarity : 0.005 0.061 837 Dihedral : 4.258 21.541 686 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -0.10 (0.35), residues: 633 helix: 1.55 (0.29), residues: 316 sheet: -1.44 (0.60), residues: 84 loop : -1.83 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 PHE 0.017 0.002 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 137 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.519 Fit side-chains REVERT: A 246 LYS cc_start: 0.8740 (tttm) cc_final: 0.8174 (tptt) REVERT: A 252 LYS cc_start: 0.7968 (tptm) cc_final: 0.7301 (tptm) REVERT: A 319 CYS cc_start: 0.8383 (m) cc_final: 0.8157 (t) REVERT: C 30 MET cc_start: 0.6872 (ptm) cc_final: 0.6596 (ptm) REVERT: C 58 ASN cc_start: 0.8593 (p0) cc_final: 0.8240 (p0) REVERT: B 47 PHE cc_start: 0.8583 (t80) cc_final: 0.8300 (t80) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1340 time to fit residues: 24.7041 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 : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.0870 chunk 41 optimal weight: 10.0000 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 32 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4942 Z= 0.197 Angle : 0.609 9.933 6721 Z= 0.315 Chirality : 0.043 0.186 795 Planarity : 0.005 0.050 837 Dihedral : 4.244 21.276 686 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % 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 : 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: -0.13 (0.35), residues: 633 helix: 1.53 (0.29), residues: 316 sheet: -1.56 (0.60), residues: 84 loop : -1.80 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 53 HIS 0.001 0.001 HIS B 31 PHE 0.018 0.001 PHE C 50 TYR 0.011 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 137 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.640 Fit side-chains REVERT: A 89 MET cc_start: 0.7709 (tpt) cc_final: 0.7381 (ttp) REVERT: A 246 LYS cc_start: 0.8715 (tttm) cc_final: 0.8236 (tptt) REVERT: A 319 CYS cc_start: 0.8337 (m) cc_final: 0.8095 (t) REVERT: C 30 MET cc_start: 0.6826 (ptm) cc_final: 0.6569 (ptm) REVERT: C 58 ASN cc_start: 0.8725 (p0) cc_final: 0.8374 (p0) REVERT: B 47 PHE cc_start: 0.8617 (t80) cc_final: 0.8283 (t80) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1566 time to fit residues: 29.1128 Evaluate side-chains 116 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.0570 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 0.0040 chunk 15 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 0.3908 ------------------------------------------------------------------------------- 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 C 73 ASN C 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2596 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= 0.188 Angle : 0.635 10.137 6721 Z= 0.321 Chirality : 0.043 0.180 795 Planarity : 0.005 0.062 837 Dihedral : 4.254 22.379 686 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % 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: -0.03 (0.35), residues: 633 helix: 1.60 (0.29), residues: 315 sheet: -1.57 (0.60), residues: 84 loop : -1.69 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 53 HIS 0.001 0.001 HIS B 31 PHE 0.018 0.001 PHE C 50 TYR 0.020 0.001 TYR A 185 ARG 0.008 0.000 ARG A 109 ********************** 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 143 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.583 Fit side-chains REVERT: A 319 CYS cc_start: 0.8305 (m) cc_final: 0.8027 (t) REVERT: A 372 MET cc_start: 0.8942 (mmm) cc_final: 0.8571 (tpt) REVERT: A 385 ILE cc_start: 0.7879 (tp) cc_final: 0.7602 (tp) REVERT: C 30 MET cc_start: 0.6915 (ptm) cc_final: 0.6653 (ptm) REVERT: C 58 ASN cc_start: 0.8668 (p0) cc_final: 0.8315 (p0) REVERT: B 47 PHE cc_start: 0.8594 (t80) cc_final: 0.8303 (t80) outliers start: 1 outliers final: 1 residues processed: 142 average time/residue: 0.1397 time to fit residues: 26.6399 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 : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.0370 chunk 51 optimal weight: 10.0000 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.166246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.140694 restraints weight = 6962.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.139803 restraints weight = 6521.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.140269 restraints weight = 6985.294| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2664 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= 0.178 Angle : 0.603 9.900 6721 Z= 0.308 Chirality : 0.043 0.174 795 Planarity : 0.005 0.062 837 Dihedral : 4.190 21.824 686 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % 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: 0.06 (0.35), residues: 633 helix: 1.73 (0.29), residues: 314 sheet: -1.71 (0.58), residues: 88 loop : -1.62 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 229 HIS 0.001 0.001 HIS B 31 PHE 0.018 0.001 PHE C 50 TYR 0.010 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: 1422.70 seconds wall clock time: 26 minutes 40.32 seconds (1600.32 seconds total)