Starting phenix.real_space_refine on Thu Sep 26 02:38:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zw1_14991/09_2024/7zw1_14991.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zw1_14991/09_2024/7zw1_14991.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/7zw1_14991/09_2024/7zw1_14991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zw1_14991/09_2024/7zw1_14991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zw1_14991/09_2024/7zw1_14991.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zw1_14991/09_2024/7zw1_14991.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= 0.007 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 S 35 5.16 5 C 3796 2.51 5 N 1018 2.21 5 O 1075 1.98 5 H 5883 0.53 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-5461/modules/chem_data/mon_lib" Total number of atoms: 11807 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 5117 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 11, 'TRANS': 305} Chain: "B" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4759 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 19, 'TRANS': 296} Chain: "C" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1931 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Time building chain proxies: 6.92, per 1000 atoms: 0.59 Number of scatterers: 11807 At special positions: 0 Unit cell: (69.536, 120.048, 139.072, 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 35 16.00 O 1075 8.00 N 1018 7.00 C 3796 6.00 H 5883 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " 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: 3.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 4 sheets defined 61.4% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 9 through 48 removed outlier: 3.694A pdb=" N ARG A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 87 removed outlier: 3.920A pdb=" N ASP A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 93 removed outlier: 4.398A pdb=" N ARG A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 97 through 122 removed outlier: 3.699A pdb=" N PHE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 140 removed outlier: 4.326A pdb=" N LEU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 removed outlier: 4.271A pdb=" N LYS A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 189 through 199 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.621A pdb=" N HIS A 233 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 293 Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'B' and resid 10 through 48 removed outlier: 4.121A pdb=" N HIS B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 60 through 89 removed outlier: 3.727A pdb=" N GLN B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 97 Proline residue: B 94 - end of helix Processing helix chain 'B' and resid 99 through 143 Proline residue: B 126 - end of helix removed outlier: 3.747A pdb=" N LEU B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 167 removed outlier: 4.431A pdb=" N ARG B 157 " --> pdb=" O CYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 203 through 206 removed outlier: 3.776A pdb=" N LEU B 206 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 203 through 206' Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 252 through 297 removed outlier: 3.876A pdb=" N GLY B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 9 Processing sheet with id=AA3, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.608A pdb=" N VAL C 14 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N CYS C 40 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE C 49 " --> pdb=" O CYS C 40 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP C 61 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.608A pdb=" N VAL C 14 " --> pdb=" O SER C 127 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1041 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: 4.20 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5874 1.03 - 1.23: 9 1.23 - 1.42: 2584 1.42 - 1.62: 3436 1.62 - 1.81: 47 Bond restraints: 11950 Sorted by residual: bond pdb=" CA GLN B 246 " pdb=" CB GLN B 246 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.44e-02 4.82e+03 6.01e-01 bond pdb=" CA ASN B 247 " pdb=" CB ASN B 247 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 4.99e-01 bond pdb=" N LEU B 9 " pdb=" CA LEU B 9 " ideal model delta sigma weight residual 1.463 1.454 0.008 1.22e-02 6.72e+03 4.83e-01 bond pdb=" CA TYR B 174 " pdb=" CB TYR B 174 " ideal model delta sigma weight residual 1.536 1.526 0.010 1.46e-02 4.69e+03 4.79e-01 bond pdb=" CA GLY B 170 " pdb=" C GLY B 170 " ideal model delta sigma weight residual 1.514 1.524 -0.009 1.41e-02 5.03e+03 4.27e-01 ... (remaining 11945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 21420 1.81 - 3.62: 135 3.62 - 5.42: 17 5.42 - 7.23: 1 7.23 - 9.04: 1 Bond angle restraints: 21574 Sorted by residual: angle pdb=" CB MET C 85 " pdb=" CG MET C 85 " pdb=" SD MET C 85 " ideal model delta sigma weight residual 112.70 121.74 -9.04 3.00e+00 1.11e-01 9.08e+00 angle pdb=" CA TYR C 106 " pdb=" CB TYR C 106 " pdb=" CG TYR C 106 " ideal model delta sigma weight residual 113.90 118.76 -4.86 1.80e+00 3.09e-01 7.30e+00 angle pdb=" CA VAL B 212 " pdb=" C VAL B 212 " pdb=" N PRO B 213 " ideal model delta sigma weight residual 117.00 119.10 -2.10 9.50e-01 1.11e+00 4.88e+00 angle pdb=" CA MET C 85 " pdb=" CB MET C 85 " pdb=" CG MET C 85 " ideal model delta sigma weight residual 114.10 118.39 -4.29 2.00e+00 2.50e-01 4.59e+00 angle pdb=" CB MET A 265 " pdb=" CG MET A 265 " pdb=" SD MET A 265 " ideal model delta sigma weight residual 112.70 118.60 -5.90 3.00e+00 1.11e-01 3.87e+00 ... (remaining 21569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4910 18.00 - 36.00: 456 36.00 - 53.99: 220 53.99 - 71.99: 43 71.99 - 89.99: 7 Dihedral angle restraints: 5636 sinusoidal: 3043 harmonic: 2593 Sorted by residual: dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 222 " pdb=" CB CYS A 222 " ideal model delta sinusoidal sigma weight residual 93.00 44.92 48.08 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CB CYS B 169 " pdb=" SG CYS B 169 " pdb=" SG CYS B 216 " pdb=" CB CYS B 216 " ideal model delta sinusoidal sigma weight residual 93.00 138.31 -45.31 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " pdb=" SG CYS C 98 " pdb=" CB CYS C 98 " ideal model delta sinusoidal sigma weight residual 93.00 51.80 41.20 1 1.00e+01 1.00e-02 2.38e+01 ... (remaining 5633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 694 0.033 - 0.065: 136 0.065 - 0.098: 57 0.098 - 0.130: 17 0.130 - 0.163: 3 Chirality restraints: 907 Sorted by residual: chirality pdb=" CA MET C 85 " pdb=" N MET C 85 " pdb=" C MET C 85 " pdb=" CB MET C 85 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CA VAL B 149 " pdb=" N VAL B 149 " pdb=" C VAL B 149 " pdb=" CB VAL B 149 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL C 53 " pdb=" N VAL C 53 " pdb=" C VAL C 53 " pdb=" CB VAL C 53 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 904 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 106 " 0.018 2.00e-02 2.50e+03 1.02e-02 3.11e+00 pdb=" CG TYR C 106 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 106 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 106 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 106 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 106 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 106 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 106 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR C 106 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR C 106 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR C 106 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR C 106 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 62 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PRO B 63 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 63 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 63 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 253 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C CYS B 253 " -0.018 2.00e-02 2.50e+03 pdb=" O CYS B 253 " 0.007 2.00e-02 2.50e+03 pdb=" N HIS B 254 " 0.006 2.00e-02 2.50e+03 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 1330 2.23 - 2.82: 25687 2.82 - 3.41: 32081 3.41 - 4.01: 40716 4.01 - 4.60: 62067 Nonbonded interactions: 161881 Sorted by model distance: nonbonded pdb="HH21 ARG B 171 " pdb=" O TYR C 106 " model vdw 1.634 2.450 nonbonded pdb=" OD1 ASP A 9 " pdb=" H LYS A 12 " model vdw 1.643 2.450 nonbonded pdb=" OD1 ASP A 237 " pdb=" H THR A 240 " model vdw 1.655 2.450 nonbonded pdb="HD22 ASN B 202 " pdb=" O LEU B 206 " model vdw 1.659 2.450 nonbonded pdb=" O VAL B 81 " pdb=" HG SER B 84 " model vdw 1.661 2.450 ... (remaining 161876 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: 5.150 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: 0.200 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.320 Find NCS groups from input model: 0.100 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.002 0.030 6067 Z= 0.146 Angle : 0.497 9.040 8239 Z= 0.258 Chirality : 0.035 0.163 907 Planarity : 0.003 0.039 1050 Dihedral : 17.278 89.990 2182 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.16 % Allowed : 22.87 % Favored : 76.97 % 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: 3.09 (0.32), residues: 754 helix: 3.84 (0.25), residues: 378 sheet: 0.70 (0.67), residues: 58 loop : 0.06 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 61 HIS 0.004 0.001 HIS C 54 PHE 0.009 0.001 PHE B 239 TYR 0.029 0.001 TYR C 106 ARG 0.003 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.4629 time to fit residues: 20.5248 Evaluate side-chains 30 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 29 optimal weight: 30.0000 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6067 Z= 0.215 Angle : 0.501 4.976 8239 Z= 0.261 Chirality : 0.035 0.135 907 Planarity : 0.004 0.047 1050 Dihedral : 3.712 19.931 828 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.63 % Allowed : 22.87 % Favored : 76.50 % 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: 2.89 (0.31), residues: 754 helix: 3.69 (0.25), residues: 380 sheet: 0.72 (0.67), residues: 58 loop : -0.13 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 61 HIS 0.004 0.001 HIS B 172 PHE 0.014 0.001 PHE B 239 TYR 0.030 0.001 TYR C 106 ARG 0.011 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 GLU cc_start: 0.8853 (tp30) cc_final: 0.8444 (tp30) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.4015 time to fit residues: 18.7125 Evaluate side-chains 34 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain C residue 106 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.8149 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6067 Z= 0.215 Angle : 0.495 5.609 8239 Z= 0.258 Chirality : 0.035 0.133 907 Planarity : 0.004 0.054 1050 Dihedral : 3.769 19.718 828 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.58 % Allowed : 22.87 % Favored : 75.55 % 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: 2.79 (0.31), residues: 754 helix: 3.61 (0.25), residues: 380 sheet: 0.72 (0.67), residues: 58 loop : -0.19 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 61 HIS 0.004 0.001 HIS C 54 PHE 0.015 0.001 PHE B 239 TYR 0.033 0.001 TYR C 106 ARG 0.008 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 GLU cc_start: 0.8895 (tp30) cc_final: 0.8452 (tp30) REVERT: C 110 MET cc_start: 0.5672 (mmt) cc_final: 0.5348 (mmt) outliers start: 10 outliers final: 4 residues processed: 41 average time/residue: 0.3748 time to fit residues: 21.5005 Evaluate side-chains 36 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain C residue 106 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 45 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 0.0670 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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: 0.8121 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6067 Z= 0.148 Angle : 0.475 5.421 8239 Z= 0.244 Chirality : 0.035 0.134 907 Planarity : 0.004 0.054 1050 Dihedral : 3.698 20.215 828 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.42 % Allowed : 23.34 % Favored : 75.24 % 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: 2.99 (0.31), residues: 754 helix: 3.77 (0.25), residues: 380 sheet: 0.75 (0.68), residues: 58 loop : -0.09 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 61 HIS 0.002 0.001 HIS C 54 PHE 0.010 0.001 PHE B 239 TYR 0.033 0.001 TYR C 106 ARG 0.008 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 MET cc_start: 0.5661 (mmt) cc_final: 0.5398 (mmt) outliers start: 9 outliers final: 6 residues processed: 43 average time/residue: 0.3584 time to fit residues: 21.5476 Evaluate side-chains 38 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain C residue 106 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.8175 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6067 Z= 0.270 Angle : 0.522 5.472 8239 Z= 0.276 Chirality : 0.035 0.133 907 Planarity : 0.004 0.059 1050 Dihedral : 3.847 20.116 828 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.58 % Allowed : 23.97 % Favored : 74.45 % 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: 2.72 (0.31), residues: 754 helix: 3.59 (0.25), residues: 380 sheet: 0.62 (0.67), residues: 58 loop : -0.26 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 61 HIS 0.004 0.001 HIS B 236 PHE 0.016 0.001 PHE B 239 TYR 0.035 0.001 TYR C 106 ARG 0.007 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 GLU cc_start: 0.8887 (tp30) cc_final: 0.8611 (tp30) REVERT: C 110 MET cc_start: 0.5838 (mmt) cc_final: 0.5486 (mmt) outliers start: 10 outliers final: 8 residues processed: 42 average time/residue: 0.3911 time to fit residues: 22.8571 Evaluate side-chains 39 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 116 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6067 Z= 0.270 Angle : 0.525 5.604 8239 Z= 0.278 Chirality : 0.036 0.130 907 Planarity : 0.004 0.059 1050 Dihedral : 3.960 19.740 828 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.52 % Allowed : 23.66 % Favored : 73.82 % 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: 2.55 (0.31), residues: 754 helix: 3.44 (0.25), residues: 379 sheet: 0.49 (0.67), residues: 58 loop : -0.31 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 61 HIS 0.003 0.001 HIS B 236 PHE 0.015 0.001 PHE A 319 TYR 0.037 0.001 TYR C 106 ARG 0.006 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 34 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 CYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8766 (p) REVERT: B 135 GLU cc_start: 0.8949 (tp30) cc_final: 0.8657 (tp30) outliers start: 16 outliers final: 12 residues processed: 48 average time/residue: 0.3406 time to fit residues: 23.2821 Evaluate side-chains 44 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 116 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 40 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6067 Z= 0.153 Angle : 0.488 5.601 8239 Z= 0.251 Chirality : 0.035 0.133 907 Planarity : 0.004 0.058 1050 Dihedral : 3.817 20.909 828 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.58 % Allowed : 24.29 % Favored : 74.13 % 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: 2.85 (0.31), residues: 754 helix: 3.66 (0.25), residues: 379 sheet: 0.58 (0.66), residues: 58 loop : -0.11 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 61 HIS 0.002 0.001 HIS B 236 PHE 0.009 0.001 PHE B 239 TYR 0.037 0.001 TYR C 106 ARG 0.007 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 GLU cc_start: 0.8867 (tp30) cc_final: 0.8582 (tp30) REVERT: C 110 MET cc_start: 0.6052 (mmt) cc_final: 0.5773 (mmt) outliers start: 10 outliers final: 9 residues processed: 41 average time/residue: 0.3442 time to fit residues: 19.9214 Evaluate side-chains 40 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 106 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- 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: 0.8152 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6067 Z= 0.177 Angle : 0.485 5.296 8239 Z= 0.251 Chirality : 0.035 0.133 907 Planarity : 0.004 0.058 1050 Dihedral : 3.781 21.847 828 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.05 % Allowed : 23.97 % Favored : 73.97 % 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: 2.87 (0.32), residues: 754 helix: 3.70 (0.25), residues: 379 sheet: 0.56 (0.66), residues: 58 loop : -0.12 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 61 HIS 0.003 0.001 HIS B 236 PHE 0.012 0.001 PHE B 239 TYR 0.035 0.001 TYR C 106 ARG 0.007 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 CYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8766 (p) REVERT: B 134 GLU cc_start: 0.8777 (tp30) cc_final: 0.8537 (tp30) REVERT: B 135 GLU cc_start: 0.8887 (tp30) cc_final: 0.8589 (tp30) REVERT: C 110 MET cc_start: 0.6057 (mmt) cc_final: 0.5778 (mmt) outliers start: 13 outliers final: 11 residues processed: 44 average time/residue: 0.3780 time to fit residues: 23.6704 Evaluate side-chains 43 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 116 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.8139 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6067 Z= 0.157 Angle : 0.476 5.174 8239 Z= 0.245 Chirality : 0.035 0.133 907 Planarity : 0.004 0.057 1050 Dihedral : 3.717 22.363 828 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.89 % Allowed : 24.29 % Favored : 73.82 % 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: 2.95 (0.32), residues: 754 helix: 3.75 (0.25), residues: 379 sheet: 0.62 (0.66), residues: 58 loop : -0.06 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 61 HIS 0.002 0.001 HIS B 236 PHE 0.010 0.001 PHE B 239 TYR 0.034 0.001 TYR C 106 ARG 0.006 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 30 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 CYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8773 (p) REVERT: B 134 GLU cc_start: 0.8787 (tp30) cc_final: 0.8553 (tp30) REVERT: B 135 GLU cc_start: 0.8875 (tp30) cc_final: 0.8574 (tp30) REVERT: C 110 MET cc_start: 0.5911 (mmt) cc_final: 0.5649 (mmt) outliers start: 12 outliers final: 10 residues processed: 42 average time/residue: 0.3400 time to fit residues: 20.0954 Evaluate side-chains 42 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 106 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6067 Z= 0.138 Angle : 0.471 6.999 8239 Z= 0.240 Chirality : 0.035 0.135 907 Planarity : 0.004 0.057 1050 Dihedral : 3.621 23.219 828 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.89 % Allowed : 24.13 % Favored : 73.97 % 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: 3.10 (0.32), residues: 754 helix: 3.84 (0.25), residues: 380 sheet: 0.59 (0.66), residues: 58 loop : 0.05 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 61 HIS 0.002 0.001 HIS B 172 PHE 0.008 0.001 PHE B 239 TYR 0.033 0.001 TYR C 106 ARG 0.007 0.000 ARG B 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.7776 (ttp) cc_final: 0.7518 (mtt) REVERT: A 118 CYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8767 (p) REVERT: B 135 GLU cc_start: 0.8840 (tp30) cc_final: 0.8509 (tp30) REVERT: C 110 MET cc_start: 0.5858 (mmt) cc_final: 0.5587 (mmt) outliers start: 12 outliers final: 9 residues processed: 44 average time/residue: 0.3760 time to fit residues: 22.8885 Evaluate side-chains 42 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 116 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.062258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.051059 restraints weight = 102852.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.052846 restraints weight = 42904.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.053976 restraints weight = 23942.594| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6067 Z= 0.156 Angle : 0.478 6.357 8239 Z= 0.246 Chirality : 0.035 0.197 907 Planarity : 0.004 0.057 1050 Dihedral : 3.603 23.409 828 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.74 % Allowed : 24.61 % Favored : 73.66 % 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: 3.09 (0.32), residues: 754 helix: 3.84 (0.25), residues: 380 sheet: 0.59 (0.66), residues: 58 loop : 0.04 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 61 HIS 0.002 0.001 HIS B 236 PHE 0.019 0.001 PHE A 275 TYR 0.033 0.001 TYR C 106 ARG 0.006 0.000 ARG B 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2759.47 seconds wall clock time: 51 minutes 23.72 seconds (3083.72 seconds total)