Starting phenix.real_space_refine on Mon Sep 23 14:08:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/09_2024/7pqg_13593.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/09_2024/7pqg_13593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/09_2024/7pqg_13593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/09_2024/7pqg_13593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/09_2024/7pqg_13593.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/09_2024/7pqg_13593.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 2134 2.51 5 N 522 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3251 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 955 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2296 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Time building chain proxies: 2.88, per 1000 atoms: 0.89 Number of scatterers: 3251 At special positions: 0 Unit cell: (61.488, 75.6, 99.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 564 8.00 N 522 7.00 C 2134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 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: 0.80 Conformation dependent library (CDL) restraints added in 494.8 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 67.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.715A pdb=" N ASP B 90 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.610A pdb=" N TYR B 113 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 44 removed outlier: 4.031A pdb=" N ASP A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.588A pdb=" N ALA A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 removed outlier: 3.686A pdb=" N MET A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 102 through 113 Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.970A pdb=" N SER A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix removed outlier: 3.785A pdb=" N ARG A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.475A pdb=" N ASP A 152 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 179 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 210 removed outlier: 3.590A pdb=" N VAL A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 removed outlier: 4.281A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.568A pdb=" N CYS A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.535A pdb=" N LEU A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 4 removed outlier: 3.800A pdb=" N MET B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 20 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.933A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 98 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 115 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.707A pdb=" N VAL B 122 " --> pdb=" O ALA B 92 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.81 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 863 1.33 - 1.45: 598 1.45 - 1.57: 1814 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 3324 Sorted by residual: bond pdb=" CG GLN A 293 " pdb=" CD GLN A 293 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.06e+00 bond pdb=" N LYS A 189 " pdb=" CA LYS A 189 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.58e+00 bond pdb=" C VAL A 187 " pdb=" N ILE A 188 " ideal model delta sigma weight residual 1.335 1.321 0.014 1.26e-02 6.30e+03 1.21e+00 bond pdb=" CB CYS A 125 " pdb=" SG CYS A 125 " ideal model delta sigma weight residual 1.808 1.773 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" N THR A 13 " pdb=" CA THR A 13 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.94e-01 ... (remaining 3319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 4194 1.58 - 3.17: 244 3.17 - 4.75: 49 4.75 - 6.33: 17 6.33 - 7.91: 2 Bond angle restraints: 4506 Sorted by residual: angle pdb=" N VAL A 187 " pdb=" CA VAL A 187 " pdb=" C VAL A 187 " ideal model delta sigma weight residual 110.62 114.37 -3.75 1.02e+00 9.61e-01 1.35e+01 angle pdb=" N GLN A 293 " pdb=" CA GLN A 293 " pdb=" CB GLN A 293 " ideal model delta sigma weight residual 110.28 115.50 -5.22 1.55e+00 4.16e-01 1.14e+01 angle pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" C ILE A 188 " ideal model delta sigma weight residual 110.62 114.01 -3.39 1.02e+00 9.61e-01 1.10e+01 angle pdb=" N GLN A 261 " pdb=" CA GLN A 261 " pdb=" C GLN A 261 " ideal model delta sigma weight residual 109.96 114.98 -5.02 1.58e+00 4.01e-01 1.01e+01 angle pdb=" N TYR A 186 " pdb=" CA TYR A 186 " pdb=" C TYR A 186 " ideal model delta sigma weight residual 113.50 109.63 3.87 1.23e+00 6.61e-01 9.89e+00 ... (remaining 4501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 1809 17.01 - 34.02: 131 34.02 - 51.03: 22 51.03 - 68.04: 3 68.04 - 85.05: 3 Dihedral angle restraints: 1968 sinusoidal: 758 harmonic: 1210 Sorted by residual: 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 93.00 164.83 -71.83 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CA LYS A 309 " pdb=" C LYS A 309 " pdb=" N PHE A 310 " pdb=" CA PHE A 310 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLU B 89 " pdb=" C GLU B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta harmonic sigma weight residual -180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 1965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 335 0.037 - 0.074: 120 0.074 - 0.112: 50 0.112 - 0.149: 19 0.149 - 0.186: 3 Chirality restraints: 527 Sorted by residual: chirality pdb=" CB ILE A 88 " pdb=" CA ILE A 88 " pdb=" CG1 ILE A 88 " pdb=" CG2 ILE A 88 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA MET A 229 " pdb=" N MET A 229 " pdb=" C MET A 229 " pdb=" CB MET A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CG LEU A 79 " pdb=" CB LEU A 79 " pdb=" CD1 LEU A 79 " pdb=" CD2 LEU A 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 524 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 109 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 110 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 289 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C TYR A 289 " -0.033 2.00e-02 2.50e+03 pdb=" O TYR A 289 " 0.012 2.00e-02 2.50e+03 pdb=" N MET A 290 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 36 " -0.011 2.00e-02 2.50e+03 1.33e-02 3.08e+00 pdb=" CG PHE A 36 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 36 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 36 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 36 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 36 " -0.001 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 389 2.74 - 3.28: 3900 3.28 - 3.82: 5577 3.82 - 4.36: 6655 4.36 - 4.90: 10332 Nonbonded interactions: 26853 Sorted by model distance: nonbonded pdb=" O THR A 124 " pdb=" OG1 THR A 127 " model vdw 2.204 3.040 nonbonded pdb=" O TRP B 53 " pdb=" NH2 ARG B 72 " model vdw 2.223 3.120 nonbonded pdb=" O LYS A 113 " pdb=" NH2 ARG A 249 " model vdw 2.225 3.120 nonbonded pdb=" OG SER B 7 " pdb=" OG SER B 21 " model vdw 2.247 3.040 nonbonded pdb=" O ILE A 168 " pdb=" OG1 THR A 171 " model vdw 2.252 3.040 ... (remaining 26848 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: 1.610 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.650 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3324 Z= 0.271 Angle : 0.880 7.914 4506 Z= 0.481 Chirality : 0.049 0.186 527 Planarity : 0.006 0.049 551 Dihedral : 12.564 85.048 1195 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 28.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.44 % 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: -0.87 (0.41), residues: 419 helix: 0.44 (0.32), residues: 241 sheet: -3.49 (0.73), residues: 34 loop : -1.44 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 116 HIS 0.003 0.001 HIS A 54 PHE 0.031 0.003 PHE A 36 TYR 0.018 0.002 TYR A 69 ARG 0.013 0.002 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7405 (mmm160) REVERT: B 93 LEU cc_start: 0.8568 (tp) cc_final: 0.8307 (tp) REVERT: A 36 PHE cc_start: 0.8694 (m-80) cc_final: 0.8474 (m-80) REVERT: A 52 LYS cc_start: 0.8498 (mtmm) cc_final: 0.7612 (tppt) REVERT: A 108 PHE cc_start: 0.9052 (m-80) cc_final: 0.8737 (m-80) REVERT: A 129 LEU cc_start: 0.8905 (mm) cc_final: 0.8299 (mm) REVERT: A 133 MET cc_start: 0.8119 (mpp) cc_final: 0.7717 (mpp) REVERT: A 215 MET cc_start: 0.8918 (mpp) cc_final: 0.8576 (mpp) REVERT: A 234 PHE cc_start: 0.8544 (m-80) cc_final: 0.8226 (m-80) REVERT: A 288 LEU cc_start: 0.9295 (mt) cc_final: 0.8965 (mt) REVERT: A 290 MET cc_start: 0.8966 (tmm) cc_final: 0.8710 (tmm) REVERT: A 291 ILE cc_start: 0.9400 (pt) cc_final: 0.8852 (pt) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1646 time to fit residues: 28.0187 Evaluate side-chains 118 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN B 39 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3324 Z= 0.309 Angle : 0.882 8.706 4506 Z= 0.466 Chirality : 0.052 0.200 527 Planarity : 0.006 0.054 551 Dihedral : 5.799 20.337 454 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 30.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.24 % Allowed : 13.45 % Favored : 84.31 % 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: -1.03 (0.41), residues: 419 helix: 0.33 (0.32), residues: 251 sheet: -2.64 (0.73), residues: 44 loop : -1.86 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 36 HIS 0.003 0.002 HIS A 54 PHE 0.027 0.003 PHE A 128 TYR 0.020 0.002 TYR B 59 ARG 0.005 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.8541 (pm20) cc_final: 0.8324 (pm20) REVERT: B 45 ARG cc_start: 0.7106 (tmm-80) cc_final: 0.6128 (tmm-80) REVERT: A 36 PHE cc_start: 0.8679 (m-80) cc_final: 0.8476 (m-80) REVERT: A 38 ILE cc_start: 0.9674 (pt) cc_final: 0.9472 (pt) REVERT: A 104 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.7581 (pp) REVERT: A 108 PHE cc_start: 0.9067 (m-80) cc_final: 0.8523 (m-80) REVERT: A 112 MET cc_start: 0.7710 (ppp) cc_final: 0.6340 (ppp) REVERT: A 129 LEU cc_start: 0.8924 (mm) cc_final: 0.8121 (mm) REVERT: A 133 MET cc_start: 0.8223 (mpp) cc_final: 0.7976 (mpp) REVERT: A 215 MET cc_start: 0.8823 (mpp) cc_final: 0.8515 (mpp) REVERT: A 221 HIS cc_start: 0.8065 (m-70) cc_final: 0.7644 (m-70) REVERT: A 264 GLN cc_start: 0.8878 (mp10) cc_final: 0.8597 (mp10) REVERT: A 290 MET cc_start: 0.8908 (tmm) cc_final: 0.8583 (tmm) REVERT: A 291 ILE cc_start: 0.9429 (pt) cc_final: 0.8722 (pt) outliers start: 8 outliers final: 5 residues processed: 137 average time/residue: 0.1541 time to fit residues: 25.5424 Evaluate side-chains 120 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 GLN Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 229 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3324 Z= 0.254 Angle : 0.876 11.257 4506 Z= 0.452 Chirality : 0.053 0.320 527 Planarity : 0.005 0.052 551 Dihedral : 5.616 20.560 454 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.36 % Allowed : 16.81 % Favored : 79.83 % 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: -0.97 (0.41), residues: 419 helix: 0.32 (0.32), residues: 251 sheet: -2.35 (0.77), residues: 44 loop : -1.81 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 56 HIS 0.002 0.001 HIS A 54 PHE 0.026 0.002 PHE A 128 TYR 0.026 0.002 TYR B 32 ARG 0.006 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 MET cc_start: 0.7909 (ppp) cc_final: 0.7375 (ppp) REVERT: B 93 LEU cc_start: 0.8901 (tp) cc_final: 0.8382 (tp) REVERT: A 35 LEU cc_start: 0.9409 (mt) cc_final: 0.9139 (mt) REVERT: A 36 PHE cc_start: 0.8650 (m-80) cc_final: 0.8446 (m-80) REVERT: A 104 LEU cc_start: 0.8616 (pt) cc_final: 0.7565 (pp) REVERT: A 108 PHE cc_start: 0.9007 (m-80) cc_final: 0.8462 (m-80) REVERT: A 112 MET cc_start: 0.7594 (ppp) cc_final: 0.6049 (ppp) REVERT: A 129 LEU cc_start: 0.8912 (mm) cc_final: 0.8030 (mm) REVERT: A 215 MET cc_start: 0.8668 (mpp) cc_final: 0.8372 (mpp) REVERT: A 221 HIS cc_start: 0.8146 (m-70) cc_final: 0.7928 (m170) REVERT: A 234 PHE cc_start: 0.8664 (m-80) cc_final: 0.8303 (m-80) REVERT: A 290 MET cc_start: 0.8911 (tmm) cc_final: 0.8700 (tmm) REVERT: A 291 ILE cc_start: 0.9368 (pt) cc_final: 0.8639 (pt) outliers start: 12 outliers final: 8 residues processed: 129 average time/residue: 0.1414 time to fit residues: 22.1122 Evaluate side-chains 125 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 231 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3324 Z= 0.271 Angle : 0.883 9.115 4506 Z= 0.453 Chirality : 0.053 0.332 527 Planarity : 0.005 0.040 551 Dihedral : 5.573 20.730 454 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 31.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.76 % Allowed : 19.61 % Favored : 75.63 % 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: -1.15 (0.41), residues: 419 helix: 0.24 (0.32), residues: 254 sheet: -2.52 (0.75), residues: 44 loop : -2.04 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 56 HIS 0.002 0.001 HIS A 54 PHE 0.024 0.003 PHE A 128 TYR 0.027 0.002 TYR B 32 ARG 0.006 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8014 (ttm-80) REVERT: B 76 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8496 (tptp) REVERT: B 93 LEU cc_start: 0.8918 (tp) cc_final: 0.8434 (tp) REVERT: A 108 PHE cc_start: 0.9012 (m-80) cc_final: 0.8614 (m-80) REVERT: A 112 MET cc_start: 0.7559 (ppp) cc_final: 0.6132 (ppp) REVERT: A 182 GLN cc_start: 0.8759 (mm110) cc_final: 0.8336 (mm-40) REVERT: A 215 MET cc_start: 0.8563 (mpp) cc_final: 0.8287 (mpp) REVERT: A 234 PHE cc_start: 0.8626 (m-80) cc_final: 0.8271 (m-80) REVERT: A 290 MET cc_start: 0.8929 (tmm) cc_final: 0.8703 (tmm) REVERT: A 291 ILE cc_start: 0.9378 (pt) cc_final: 0.8639 (pt) outliers start: 17 outliers final: 9 residues processed: 132 average time/residue: 0.1423 time to fit residues: 22.7699 Evaluate side-chains 125 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 231 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3324 Z= 0.255 Angle : 0.896 10.418 4506 Z= 0.457 Chirality : 0.055 0.344 527 Planarity : 0.005 0.048 551 Dihedral : 5.567 20.820 454 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 28.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.48 % Allowed : 21.85 % Favored : 73.67 % 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: -1.16 (0.41), residues: 419 helix: 0.24 (0.32), residues: 253 sheet: -2.83 (0.70), residues: 50 loop : -1.81 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 105 HIS 0.002 0.001 HIS A 221 PHE 0.056 0.003 PHE A 36 TYR 0.028 0.002 TYR B 32 ARG 0.007 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.8026 (mmm-85) cc_final: 0.7520 (mmm-85) REVERT: B 76 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8487 (tptp) REVERT: B 83 MET cc_start: 0.8344 (ptm) cc_final: 0.7891 (ppp) REVERT: B 93 LEU cc_start: 0.8903 (tp) cc_final: 0.7872 (tp) REVERT: A 31 LEU cc_start: 0.9631 (mt) cc_final: 0.9157 (pp) REVERT: A 35 LEU cc_start: 0.9333 (mt) cc_final: 0.9101 (mt) REVERT: A 108 PHE cc_start: 0.8977 (m-80) cc_final: 0.8568 (m-80) REVERT: A 112 MET cc_start: 0.7466 (ppp) cc_final: 0.5655 (ppp) REVERT: A 147 ASP cc_start: 0.8570 (m-30) cc_final: 0.8125 (p0) REVERT: A 182 GLN cc_start: 0.8719 (mm110) cc_final: 0.8325 (mm-40) REVERT: A 215 MET cc_start: 0.8591 (mpp) cc_final: 0.8118 (mpp) REVERT: A 234 PHE cc_start: 0.8612 (m-80) cc_final: 0.8315 (m-80) REVERT: A 290 MET cc_start: 0.8946 (tmm) cc_final: 0.8743 (tmm) REVERT: A 291 ILE cc_start: 0.9378 (pt) cc_final: 0.8622 (pt) outliers start: 16 outliers final: 9 residues processed: 135 average time/residue: 0.1686 time to fit residues: 26.7688 Evaluate side-chains 129 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 244 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 4 optimal weight: 0.1980 chunk 22 optimal weight: 5.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3324 Z= 0.233 Angle : 0.931 11.427 4506 Z= 0.470 Chirality : 0.056 0.350 527 Planarity : 0.005 0.040 551 Dihedral : 5.563 20.947 454 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.08 % Allowed : 28.29 % Favored : 68.63 % 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: -1.25 (0.41), residues: 419 helix: 0.14 (0.32), residues: 253 sheet: -2.89 (0.68), residues: 50 loop : -1.75 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 105 HIS 0.003 0.001 HIS A 221 PHE 0.052 0.003 PHE A 36 TYR 0.029 0.002 TYR B 32 ARG 0.007 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 LYS cc_start: 0.8839 (mtmm) cc_final: 0.8448 (tptp) REVERT: B 83 MET cc_start: 0.8311 (ptm) cc_final: 0.7757 (ppp) REVERT: B 93 LEU cc_start: 0.8893 (tp) cc_final: 0.8395 (tp) REVERT: A 83 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.5970 (t80) REVERT: A 108 PHE cc_start: 0.8956 (m-80) cc_final: 0.8670 (m-80) REVERT: A 112 MET cc_start: 0.7434 (ppp) cc_final: 0.7194 (ppp) REVERT: A 147 ASP cc_start: 0.8538 (m-30) cc_final: 0.8071 (p0) REVERT: A 182 GLN cc_start: 0.8739 (mm110) cc_final: 0.8339 (mm-40) REVERT: A 215 MET cc_start: 0.8489 (mpp) cc_final: 0.8082 (mpp) REVERT: A 221 HIS cc_start: 0.8134 (m-70) cc_final: 0.6950 (m-70) REVERT: A 234 PHE cc_start: 0.8634 (m-80) cc_final: 0.8324 (m-80) REVERT: A 243 LEU cc_start: 0.8432 (mt) cc_final: 0.8052 (mm) REVERT: A 274 PHE cc_start: 0.8133 (m-80) cc_final: 0.7534 (t80) REVERT: A 290 MET cc_start: 0.9036 (tmm) cc_final: 0.8784 (tmm) REVERT: A 291 ILE cc_start: 0.9342 (pt) cc_final: 0.8610 (pt) outliers start: 11 outliers final: 8 residues processed: 132 average time/residue: 0.1546 time to fit residues: 24.4121 Evaluate side-chains 127 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 244 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3324 Z= 0.236 Angle : 0.925 11.377 4506 Z= 0.467 Chirality : 0.056 0.366 527 Planarity : 0.005 0.039 551 Dihedral : 5.479 20.379 454 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 25.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.20 % Allowed : 27.45 % Favored : 68.35 % 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: -1.18 (0.41), residues: 419 helix: 0.17 (0.32), residues: 254 sheet: -2.80 (0.67), residues: 50 loop : -1.71 (0.61), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 105 HIS 0.002 0.001 HIS A 54 PHE 0.048 0.003 PHE A 36 TYR 0.025 0.002 TYR B 32 ARG 0.007 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.7438 (p90) cc_final: 0.7121 (p90) REVERT: B 76 LYS cc_start: 0.8841 (mtmm) cc_final: 0.8452 (tptp) REVERT: B 83 MET cc_start: 0.8149 (ptm) cc_final: 0.7076 (ppp) REVERT: B 93 LEU cc_start: 0.8887 (tp) cc_final: 0.8450 (tp) REVERT: A 46 MET cc_start: 0.8039 (tmm) cc_final: 0.5956 (mtt) REVERT: A 47 GLU cc_start: 0.9059 (pm20) cc_final: 0.8396 (pm20) REVERT: A 83 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6082 (t80) REVERT: A 108 PHE cc_start: 0.8899 (m-80) cc_final: 0.8583 (m-80) REVERT: A 112 MET cc_start: 0.7432 (ppp) cc_final: 0.7231 (ppp) REVERT: A 147 ASP cc_start: 0.8528 (m-30) cc_final: 0.8053 (p0) REVERT: A 182 GLN cc_start: 0.8661 (mm110) cc_final: 0.8232 (mm-40) REVERT: A 215 MET cc_start: 0.8483 (mpp) cc_final: 0.8084 (mpp) REVERT: A 221 HIS cc_start: 0.8192 (m-70) cc_final: 0.6982 (m-70) REVERT: A 234 PHE cc_start: 0.8637 (m-80) cc_final: 0.8315 (m-80) REVERT: A 243 LEU cc_start: 0.8413 (mt) cc_final: 0.8039 (mm) REVERT: A 264 GLN cc_start: 0.8603 (mp10) cc_final: 0.8388 (pm20) REVERT: A 274 PHE cc_start: 0.8132 (m-80) cc_final: 0.7516 (t80) REVERT: A 290 MET cc_start: 0.9066 (tmm) cc_final: 0.8859 (tmm) REVERT: A 291 ILE cc_start: 0.9377 (pt) cc_final: 0.8670 (pt) outliers start: 15 outliers final: 9 residues processed: 134 average time/residue: 0.1510 time to fit residues: 24.2072 Evaluate side-chains 129 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 244 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.0030 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3324 Z= 0.242 Angle : 0.973 11.188 4506 Z= 0.484 Chirality : 0.057 0.335 527 Planarity : 0.005 0.042 551 Dihedral : 5.482 21.542 454 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.80 % Allowed : 31.65 % Favored : 65.55 % 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: -1.26 (0.41), residues: 419 helix: 0.08 (0.32), residues: 255 sheet: -2.72 (0.67), residues: 50 loop : -1.76 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 105 HIS 0.001 0.001 HIS A 54 PHE 0.050 0.003 PHE A 36 TYR 0.023 0.002 TYR B 32 ARG 0.007 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.7531 (p90) cc_final: 0.7120 (p90) REVERT: B 76 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8495 (tptp) REVERT: B 80 TYR cc_start: 0.8287 (t80) cc_final: 0.7711 (t80) REVERT: B 83 MET cc_start: 0.7561 (ptm) cc_final: 0.7004 (ppp) REVERT: B 93 LEU cc_start: 0.8894 (tp) cc_final: 0.8466 (tp) REVERT: A 46 MET cc_start: 0.8044 (tmm) cc_final: 0.5852 (mtt) REVERT: A 47 GLU cc_start: 0.9095 (pm20) cc_final: 0.8392 (pm20) REVERT: A 83 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6092 (t80) REVERT: A 108 PHE cc_start: 0.8916 (m-80) cc_final: 0.8621 (m-80) REVERT: A 112 MET cc_start: 0.7455 (ppp) cc_final: 0.5860 (ppp) REVERT: A 147 ASP cc_start: 0.8519 (m-30) cc_final: 0.8040 (p0) REVERT: A 182 GLN cc_start: 0.8605 (mm110) cc_final: 0.8190 (mm-40) REVERT: A 215 MET cc_start: 0.8509 (mpp) cc_final: 0.8201 (mpp) REVERT: A 221 HIS cc_start: 0.8236 (m-70) cc_final: 0.7016 (m-70) REVERT: A 234 PHE cc_start: 0.8644 (m-80) cc_final: 0.8334 (m-80) REVERT: A 243 LEU cc_start: 0.8382 (mt) cc_final: 0.8009 (mm) REVERT: A 274 PHE cc_start: 0.8079 (m-80) cc_final: 0.7482 (t80) REVERT: A 290 MET cc_start: 0.9038 (tmm) cc_final: 0.8805 (tmm) REVERT: A 291 ILE cc_start: 0.9429 (pt) cc_final: 0.8825 (pt) outliers start: 10 outliers final: 9 residues processed: 127 average time/residue: 0.1486 time to fit residues: 22.8019 Evaluate side-chains 129 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 244 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 0.0670 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3324 Z= 0.250 Angle : 1.004 12.118 4506 Z= 0.507 Chirality : 0.059 0.325 527 Planarity : 0.005 0.042 551 Dihedral : 5.533 20.601 454 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.64 % Allowed : 31.93 % Favored : 64.43 % 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: -1.20 (0.41), residues: 419 helix: 0.16 (0.32), residues: 254 sheet: -2.72 (0.64), residues: 50 loop : -1.77 (0.61), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 36 HIS 0.001 0.001 HIS A 54 PHE 0.046 0.003 PHE A 36 TYR 0.022 0.002 TYR B 32 ARG 0.006 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.7537 (p90) cc_final: 0.7096 (p90) REVERT: B 67 ARG cc_start: 0.7782 (ttm-80) cc_final: 0.7423 (ttm-80) REVERT: B 76 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8468 (tptp) REVERT: B 80 TYR cc_start: 0.8289 (t80) cc_final: 0.7539 (t80) REVERT: B 93 LEU cc_start: 0.8859 (tp) cc_final: 0.8441 (tp) REVERT: A 46 MET cc_start: 0.8147 (tmm) cc_final: 0.5904 (mtt) REVERT: A 47 GLU cc_start: 0.9083 (pm20) cc_final: 0.8433 (pm20) REVERT: A 108 PHE cc_start: 0.8917 (m-80) cc_final: 0.8557 (m-80) REVERT: A 112 MET cc_start: 0.7391 (ppp) cc_final: 0.5894 (ppp) REVERT: A 147 ASP cc_start: 0.8503 (m-30) cc_final: 0.7995 (p0) REVERT: A 182 GLN cc_start: 0.8638 (mm110) cc_final: 0.8265 (mm-40) REVERT: A 215 MET cc_start: 0.8471 (mpp) cc_final: 0.8170 (mpp) REVERT: A 234 PHE cc_start: 0.8594 (m-80) cc_final: 0.8304 (m-80) REVERT: A 243 LEU cc_start: 0.8385 (mt) cc_final: 0.8014 (mm) REVERT: A 274 PHE cc_start: 0.7984 (m-80) cc_final: 0.7410 (t80) REVERT: A 291 ILE cc_start: 0.9411 (pt) cc_final: 0.8812 (pt) outliers start: 13 outliers final: 9 residues processed: 126 average time/residue: 0.1580 time to fit residues: 23.7973 Evaluate side-chains 127 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 258 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.0570 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3324 Z= 0.299 Angle : 1.060 12.260 4506 Z= 0.541 Chirality : 0.061 0.297 527 Planarity : 0.006 0.042 551 Dihedral : 5.634 21.218 454 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 32.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.52 % Allowed : 34.45 % Favored : 63.03 % 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: -1.28 (0.41), residues: 419 helix: 0.10 (0.32), residues: 254 sheet: -2.72 (0.63), residues: 50 loop : -1.85 (0.60), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 36 HIS 0.002 0.001 HIS A 54 PHE 0.047 0.003 PHE A 36 TYR 0.021 0.002 TYR B 32 ARG 0.007 0.001 ARG B 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7514 (mmm160) cc_final: 0.6972 (mmm160) REVERT: B 32 TYR cc_start: 0.7854 (p90) cc_final: 0.7332 (p90) REVERT: B 67 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7492 (ttm-80) REVERT: B 76 LYS cc_start: 0.8947 (mtmm) cc_final: 0.8501 (tptp) REVERT: B 80 TYR cc_start: 0.8324 (t80) cc_final: 0.7783 (t80) REVERT: A 46 MET cc_start: 0.8242 (tmm) cc_final: 0.6089 (mtt) REVERT: A 47 GLU cc_start: 0.9140 (pm20) cc_final: 0.8511 (pm20) REVERT: A 108 PHE cc_start: 0.8954 (m-80) cc_final: 0.8601 (m-80) REVERT: A 112 MET cc_start: 0.7513 (ppp) cc_final: 0.6012 (ppp) REVERT: A 147 ASP cc_start: 0.8582 (m-30) cc_final: 0.8084 (p0) REVERT: A 198 CYS cc_start: 0.9014 (p) cc_final: 0.8752 (p) REVERT: A 215 MET cc_start: 0.8461 (mpp) cc_final: 0.8086 (mpp) REVERT: A 221 HIS cc_start: 0.8240 (m-70) cc_final: 0.7978 (m90) REVERT: A 234 PHE cc_start: 0.8573 (m-80) cc_final: 0.8292 (m-80) REVERT: A 243 LEU cc_start: 0.8397 (mt) cc_final: 0.8018 (mm) outliers start: 9 outliers final: 8 residues processed: 123 average time/residue: 0.1568 time to fit residues: 23.1025 Evaluate side-chains 130 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 265 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.0270 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.079002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.065767 restraints weight = 14582.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.067672 restraints weight = 10195.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.069118 restraints weight = 7715.069| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3324 Z= 0.268 Angle : 1.069 13.626 4506 Z= 0.536 Chirality : 0.061 0.298 527 Planarity : 0.006 0.044 551 Dihedral : 5.589 20.561 454 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 28.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.80 % Allowed : 32.77 % Favored : 64.43 % 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: -1.24 (0.41), residues: 419 helix: 0.15 (0.32), residues: 254 sheet: -2.75 (0.63), residues: 50 loop : -1.86 (0.60), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 116 HIS 0.001 0.001 HIS A 54 PHE 0.045 0.003 PHE A 36 TYR 0.022 0.002 TYR B 32 ARG 0.007 0.001 ARG B 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1172.68 seconds wall clock time: 21 minutes 34.01 seconds (1294.01 seconds total)