Starting phenix.real_space_refine on Mon Sep 23 17:57:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc3_42114/09_2024/8uc3_42114.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc3_42114/09_2024/8uc3_42114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc3_42114/09_2024/8uc3_42114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc3_42114/09_2024/8uc3_42114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc3_42114/09_2024/8uc3_42114.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc3_42114/09_2024/8uc3_42114.cif" } resolution = 2.78 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= 0.039 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 P 2 5.49 5 S 28 5.16 5 C 2700 2.51 5 N 766 2.21 5 O 808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 4304 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1365 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 13, 'TRANS': 166} Chain: "C" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 756 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, B Time building chain proxies: 3.73, per 1000 atoms: 0.87 Number of scatterers: 4304 At special positions: 0 Unit cell: (84.87, 75.5343, 78.9291, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 2 15.00 O 808 8.00 N 766 7.00 C 2700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 563.4 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 58.3% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.801A pdb=" N ARG A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 101 through 130 removed outlier: 3.733A pdb=" N THR A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.503A pdb=" N VAL A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.855A pdb=" N VAL A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 37 through 55 removed outlier: 3.505A pdb=" N GLU D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.732A pdb=" N ARG D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 99 Processing helix chain 'D' and resid 100 through 103 Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 37 through 55 removed outlier: 3.505A pdb=" N GLU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 76 removed outlier: 3.733A pdb=" N ARG C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 99 Processing helix chain 'C' and resid 100 through 103 Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.801A pdb=" N ARG B 71 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 101 through 130 removed outlier: 3.733A pdb=" N THR B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 119 " --> pdb=" O CYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.504A pdb=" N VAL B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.855A pdb=" N VAL B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.078A pdb=" N VAL A 92 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.903A pdb=" N ASN A 183 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL B 92 " --> pdb=" O PRO B 157 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 672 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: 0.94 Time building geometry restraints manager: 1.23 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: 1176 1.33 - 1.45: 646 1.45 - 1.57: 2514 1.57 - 1.69: 2 1.69 - 1.81: 46 Bond restraints: 4384 Sorted by residual: bond pdb=" N VAL B 182 " pdb=" CA VAL B 182 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.19e-02 7.06e+03 1.21e+01 bond pdb=" N VAL A 182 " pdb=" CA VAL A 182 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.19e-02 7.06e+03 1.20e+01 bond pdb=" N THR B 23 " pdb=" CA THR B 23 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.33e-02 5.65e+03 9.73e+00 bond pdb=" N THR A 23 " pdb=" CA THR A 23 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.33e-02 5.65e+03 9.64e+00 bond pdb=" N ARG B 24 " pdb=" CA ARG B 24 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.30e-02 5.92e+03 8.57e+00 ... (remaining 4379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 5543 1.54 - 3.07: 360 3.07 - 4.61: 49 4.61 - 6.15: 14 6.15 - 7.68: 4 Bond angle restraints: 5970 Sorted by residual: angle pdb=" N THR B 23 " pdb=" CA THR B 23 " pdb=" C THR B 23 " ideal model delta sigma weight residual 112.54 118.53 -5.99 1.22e+00 6.72e-01 2.41e+01 angle pdb=" N THR A 23 " pdb=" CA THR A 23 " pdb=" C THR A 23 " ideal model delta sigma weight residual 112.54 118.49 -5.95 1.22e+00 6.72e-01 2.38e+01 angle pdb=" N ARG B 66 " pdb=" CA ARG B 66 " pdb=" C ARG B 66 " ideal model delta sigma weight residual 109.64 103.67 5.97 1.27e+00 6.20e-01 2.21e+01 angle pdb=" N ARG A 66 " pdb=" CA ARG A 66 " pdb=" C ARG A 66 " ideal model delta sigma weight residual 109.64 103.68 5.96 1.27e+00 6.20e-01 2.20e+01 angle pdb=" CA GLU A 180 " pdb=" C GLU A 180 " pdb=" O GLU A 180 " ideal model delta sigma weight residual 120.55 116.93 3.62 1.06e+00 8.90e-01 1.17e+01 ... (remaining 5965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 2345 16.90 - 33.79: 223 33.79 - 50.69: 96 50.69 - 67.58: 12 67.58 - 84.48: 8 Dihedral angle restraints: 2684 sinusoidal: 1076 harmonic: 1608 Sorted by residual: dihedral pdb=" CG ARG A 74 " pdb=" CD ARG A 74 " pdb=" NE ARG A 74 " pdb=" CZ ARG A 74 " ideal model delta sinusoidal sigma weight residual -180.00 -135.17 -44.83 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG B 74 " pdb=" CD ARG B 74 " pdb=" NE ARG B 74 " pdb=" CZ ARG B 74 " ideal model delta sinusoidal sigma weight residual 180.00 -135.19 -44.81 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ARG A 56 " pdb=" CB ARG A 56 " pdb=" CG ARG A 56 " pdb=" CD ARG A 56 " ideal model delta sinusoidal sigma weight residual -180.00 -125.98 -54.02 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 2681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 534 0.050 - 0.100: 107 0.100 - 0.149: 45 0.149 - 0.199: 0 0.199 - 0.249: 2 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA VAL A 64 " pdb=" N VAL A 64 " pdb=" C VAL A 64 " pdb=" CB VAL A 64 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA VAL B 64 " pdb=" N VAL B 64 " pdb=" C VAL B 64 " pdb=" CB VAL B 64 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CG LEU A 100 " pdb=" CB LEU A 100 " pdb=" CD1 LEU A 100 " pdb=" CD2 LEU A 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 685 not shown) Planarity restraints: 772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 179 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C ASN A 179 " 0.064 2.00e-02 2.50e+03 pdb=" O ASN A 179 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU A 180 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 179 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C ASN B 179 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN B 179 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU B 180 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 161 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO B 162 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " 0.030 5.00e-02 4.00e+02 ... (remaining 769 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 74 2.67 - 3.23: 4019 3.23 - 3.79: 6215 3.79 - 4.34: 8917 4.34 - 4.90: 14548 Nonbonded interactions: 33773 Sorted by model distance: nonbonded pdb=" OE2 GLU D 32 " pdb=" NH2 ARG B 141 " model vdw 2.115 3.120 nonbonded pdb=" OD1 ASP C 44 " pdb=" NH1 ARG C 47 " model vdw 2.321 3.120 nonbonded pdb=" OD1 ASP D 44 " pdb=" NH1 ARG D 47 " model vdw 2.321 3.120 nonbonded pdb=" NH2 ARG C 62 " pdb=" OE2 GLU C 101 " model vdw 2.343 3.120 nonbonded pdb=" NH2 ARG D 62 " pdb=" OE2 GLU D 101 " model vdw 2.343 3.120 ... (remaining 33768 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.540 Find NCS groups from input model: 0.110 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 : 0.005 0.041 4384 Z= 0.302 Angle : 0.848 7.683 5970 Z= 0.548 Chirality : 0.049 0.249 688 Planarity : 0.006 0.054 772 Dihedral : 16.433 84.478 1640 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.78 % Allowed : 22.67 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.36), residues: 548 helix: 0.58 (0.32), residues: 272 sheet: 2.34 (0.74), residues: 44 loop : -0.48 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 187 HIS 0.002 0.001 HIS B 154 PHE 0.005 0.001 PHE B 86 TYR 0.009 0.001 TYR B 109 ARG 0.004 0.001 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.494 Fit side-chains REVERT: C 62 ARG cc_start: 0.6692 (ttm170) cc_final: 0.6217 (mtp180) REVERT: C 94 GLN cc_start: 0.7342 (mt0) cc_final: 0.7056 (mt0) REVERT: B 118 MET cc_start: 0.7280 (mtt) cc_final: 0.6907 (mtt) outliers start: 8 outliers final: 2 residues processed: 89 average time/residue: 1.2351 time to fit residues: 113.7957 Evaluate side-chains 70 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 183 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.0030 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4384 Z= 0.212 Angle : 0.615 6.527 5970 Z= 0.321 Chirality : 0.042 0.139 688 Planarity : 0.006 0.053 772 Dihedral : 6.757 56.445 629 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.00 % Allowed : 20.44 % Favored : 73.56 % 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: 1.00 (0.37), residues: 548 helix: 1.17 (0.31), residues: 294 sheet: 2.05 (0.75), residues: 54 loop : -0.41 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.006 0.001 PHE A 86 TYR 0.012 0.002 TYR D 22 ARG 0.003 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 66 time to evaluate : 0.454 Fit side-chains REVERT: A 22 LYS cc_start: 0.6175 (mtmt) cc_final: 0.5924 (mptt) REVERT: D 33 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8090 (mt-10) REVERT: C 97 ASP cc_start: 0.7223 (m-30) cc_final: 0.6892 (t0) REVERT: B 108 ILE cc_start: 0.7865 (pt) cc_final: 0.7635 (pp) REVERT: B 174 GLN cc_start: 0.7109 (tp40) cc_final: 0.6903 (tp40) outliers start: 27 outliers final: 11 residues processed: 80 average time/residue: 0.9804 time to fit residues: 81.9727 Evaluate side-chains 74 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4384 Z= 0.197 Angle : 0.573 11.277 5970 Z= 0.290 Chirality : 0.040 0.133 688 Planarity : 0.006 0.053 772 Dihedral : 6.317 59.267 629 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.89 % Allowed : 19.78 % Favored : 75.33 % 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: 1.45 (0.37), residues: 548 helix: 1.60 (0.30), residues: 292 sheet: 2.03 (0.78), residues: 54 loop : -0.24 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.008 0.001 PHE A 86 TYR 0.011 0.002 TYR D 22 ARG 0.003 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 0.438 Fit side-chains REVERT: A 22 LYS cc_start: 0.6080 (mtmt) cc_final: 0.5807 (mptt) REVERT: D 33 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: D 97 ASP cc_start: 0.7725 (m-30) cc_final: 0.7464 (m-30) REVERT: B 174 GLN cc_start: 0.7172 (tp40) cc_final: 0.6564 (mp10) outliers start: 22 outliers final: 10 residues processed: 81 average time/residue: 1.2250 time to fit residues: 102.8666 Evaluate side-chains 76 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4384 Z= 0.216 Angle : 0.577 6.129 5970 Z= 0.295 Chirality : 0.040 0.137 688 Planarity : 0.006 0.057 772 Dihedral : 6.239 57.506 628 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.44 % Allowed : 20.00 % Favored : 75.56 % 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: 1.55 (0.38), residues: 548 helix: 1.68 (0.30), residues: 292 sheet: 1.97 (0.78), residues: 54 loop : -0.15 (0.48), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 18 HIS 0.002 0.001 HIS A 154 PHE 0.010 0.001 PHE A 86 TYR 0.010 0.001 TYR D 22 ARG 0.010 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 0.486 Fit side-chains REVERT: A 62 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7781 (ttp) REVERT: A 156 GLU cc_start: 0.7272 (tt0) cc_final: 0.7056 (pt0) REVERT: D 33 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: D 78 MET cc_start: 0.7483 (mtp) cc_final: 0.7263 (mtt) REVERT: B 174 GLN cc_start: 0.7273 (tp40) cc_final: 0.6584 (mp10) outliers start: 20 outliers final: 10 residues processed: 71 average time/residue: 1.2093 time to fit residues: 89.2820 Evaluate side-chains 74 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4384 Z= 0.220 Angle : 0.577 6.007 5970 Z= 0.293 Chirality : 0.040 0.138 688 Planarity : 0.006 0.061 772 Dihedral : 6.144 54.476 628 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.33 % Allowed : 21.56 % Favored : 75.11 % 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: 1.49 (0.37), residues: 548 helix: 1.66 (0.30), residues: 292 sheet: 1.80 (0.79), residues: 54 loop : -0.18 (0.48), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 18 HIS 0.002 0.001 HIS A 154 PHE 0.009 0.001 PHE A 86 TYR 0.010 0.001 TYR D 22 ARG 0.013 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.497 Fit side-chains REVERT: A 156 GLU cc_start: 0.7283 (tt0) cc_final: 0.7066 (pt0) REVERT: D 33 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: B 174 GLN cc_start: 0.7247 (tp40) cc_final: 0.5911 (pm20) outliers start: 15 outliers final: 9 residues processed: 69 average time/residue: 1.2888 time to fit residues: 92.0948 Evaluate side-chains 71 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7129 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4384 Z= 0.324 Angle : 0.680 6.971 5970 Z= 0.344 Chirality : 0.044 0.148 688 Planarity : 0.007 0.074 772 Dihedral : 6.341 54.347 628 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.33 % Allowed : 19.11 % Favored : 75.56 % 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: 1.02 (0.37), residues: 548 helix: 1.37 (0.30), residues: 286 sheet: 1.57 (0.78), residues: 54 loop : -0.49 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 18 HIS 0.003 0.001 HIS B 128 PHE 0.009 0.001 PHE A 86 TYR 0.011 0.002 TYR D 22 ARG 0.016 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 0.479 Fit side-chains REVERT: A 147 SER cc_start: 0.7358 (t) cc_final: 0.6976 (p) REVERT: D 33 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: B 174 GLN cc_start: 0.7302 (tp40) cc_final: 0.5866 (pm20) outliers start: 24 outliers final: 11 residues processed: 73 average time/residue: 1.1997 time to fit residues: 90.9679 Evaluate side-chains 73 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7100 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4384 Z= 0.252 Angle : 0.618 6.310 5970 Z= 0.314 Chirality : 0.041 0.129 688 Planarity : 0.006 0.081 772 Dihedral : 6.029 51.871 628 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.78 % Allowed : 21.11 % Favored : 75.11 % 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 (0.37), residues: 548 helix: 1.54 (0.30), residues: 286 sheet: 1.62 (0.76), residues: 52 loop : -0.52 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 18 HIS 0.002 0.001 HIS B 128 PHE 0.010 0.001 PHE A 86 TYR 0.010 0.002 TYR C 22 ARG 0.017 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.494 Fit side-chains REVERT: A 62 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7730 (ttp) REVERT: A 147 SER cc_start: 0.7344 (t) cc_final: 0.6972 (p) REVERT: A 156 GLU cc_start: 0.7373 (tt0) cc_final: 0.7049 (pt0) REVERT: D 33 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: D 72 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6784 (mt-10) REVERT: B 174 GLN cc_start: 0.7306 (tp40) cc_final: 0.5847 (pm20) outliers start: 17 outliers final: 12 residues processed: 68 average time/residue: 1.2436 time to fit residues: 87.7089 Evaluate side-chains 73 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 0.0470 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4384 Z= 0.218 Angle : 0.588 6.631 5970 Z= 0.300 Chirality : 0.040 0.127 688 Planarity : 0.006 0.079 772 Dihedral : 5.732 50.170 628 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.33 % Allowed : 22.00 % Favored : 74.67 % 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: 1.34 (0.37), residues: 548 helix: 1.63 (0.30), residues: 290 sheet: 1.68 (0.75), residues: 52 loop : -0.35 (0.47), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 18 HIS 0.002 0.001 HIS A 154 PHE 0.010 0.001 PHE A 86 TYR 0.009 0.001 TYR D 22 ARG 0.018 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.501 Fit side-chains REVERT: A 18 TRP cc_start: 0.6080 (OUTLIER) cc_final: 0.5454 (m-10) REVERT: A 62 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7742 (ttp) REVERT: A 147 SER cc_start: 0.7327 (t) cc_final: 0.6976 (p) REVERT: A 156 GLU cc_start: 0.7285 (tt0) cc_final: 0.7065 (pt0) REVERT: D 33 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: B 174 GLN cc_start: 0.7364 (tp40) cc_final: 0.5799 (pm20) outliers start: 15 outliers final: 9 residues processed: 69 average time/residue: 1.2261 time to fit residues: 87.8024 Evaluate side-chains 69 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7065 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4384 Z= 0.206 Angle : 0.588 6.908 5970 Z= 0.297 Chirality : 0.040 0.131 688 Planarity : 0.006 0.083 772 Dihedral : 5.565 49.075 626 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.89 % Allowed : 22.44 % Favored : 74.67 % 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: 1.43 (0.37), residues: 548 helix: 1.68 (0.30), residues: 290 sheet: 1.70 (0.76), residues: 52 loop : -0.25 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 18 HIS 0.002 0.001 HIS A 154 PHE 0.010 0.001 PHE A 86 TYR 0.008 0.001 TYR D 22 ARG 0.020 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.470 Fit side-chains REVERT: A 62 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7746 (ttp) REVERT: A 147 SER cc_start: 0.7316 (t) cc_final: 0.6963 (p) REVERT: D 33 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: D 90 ASP cc_start: 0.7026 (t70) cc_final: 0.6642 (t0) REVERT: B 174 GLN cc_start: 0.7354 (tp40) cc_final: 0.5804 (pm20) outliers start: 13 outliers final: 9 residues processed: 64 average time/residue: 1.3279 time to fit residues: 87.9850 Evaluate side-chains 65 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7089 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4384 Z= 0.244 Angle : 0.627 7.706 5970 Z= 0.317 Chirality : 0.041 0.133 688 Planarity : 0.006 0.090 772 Dihedral : 5.676 51.066 626 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.11 % Allowed : 21.56 % Favored : 75.33 % 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 (0.37), residues: 548 helix: 1.54 (0.30), residues: 290 sheet: 1.26 (0.75), residues: 54 loop : -0.24 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 18 HIS 0.002 0.001 HIS B 128 PHE 0.010 0.001 PHE A 86 TYR 0.010 0.002 TYR C 22 ARG 0.020 0.001 ARG A 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.452 Fit side-chains REVERT: A 18 TRP cc_start: 0.6052 (OUTLIER) cc_final: 0.5438 (m-90) REVERT: A 62 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7731 (ttp) REVERT: A 147 SER cc_start: 0.7321 (t) cc_final: 0.6962 (p) REVERT: D 33 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: D 72 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6735 (mt-10) REVERT: C 95 MET cc_start: 0.5516 (mmm) cc_final: 0.4392 (tpt) REVERT: B 174 GLN cc_start: 0.7346 (tp40) cc_final: 0.5737 (pm20) outliers start: 14 outliers final: 11 residues processed: 65 average time/residue: 1.2045 time to fit residues: 81.3896 Evaluate side-chains 69 residues out of total 450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.0870 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.185419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144261 restraints weight = 4712.755| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.13 r_work: 0.3701 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4384 Z= 0.187 Angle : 0.571 7.201 5970 Z= 0.290 Chirality : 0.040 0.127 688 Planarity : 0.006 0.086 772 Dihedral : 5.402 47.060 626 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.89 % Allowed : 21.78 % Favored : 75.33 % 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: 1.58 (0.38), residues: 548 helix: 1.81 (0.30), residues: 290 sheet: 1.61 (0.76), residues: 52 loop : -0.15 (0.49), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.010 0.001 PHE A 86 TYR 0.007 0.001 TYR C 22 ARG 0.020 0.001 ARG A 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.01 seconds wall clock time: 38 minutes 21.89 seconds (2301.89 seconds total)