Starting phenix.real_space_refine on Tue Feb 13 07:57:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/02_2024/7sk1_25169_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/02_2024/7sk1_25169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/02_2024/7sk1_25169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/02_2024/7sk1_25169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/02_2024/7sk1_25169_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/02_2024/7sk1_25169_updated.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 18 5.16 5 C 2880 2.51 5 N 666 2.21 5 O 724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 65": "OE1" <-> "OE2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B GLU 265": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4291 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2122 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 7, 'TRANS': 254} Chain: "B" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2122 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 7, 'TRANS': 254} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Unusual residues: {' K': 3, 'C14': 1, 'OCT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'C14': 1, 'OCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.91, per 1000 atoms: 0.68 Number of scatterers: 4291 At special positions: 0 Unit cell: (70.245, 56.865, 98.12, 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) K 3 19.00 S 18 16.00 O 724 8.00 N 666 7.00 C 2880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS B 69 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 788.5 milliseconds 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 0 sheets defined 77.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 21 through 67 removed outlier: 3.505A pdb=" N VAL A 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 46 " --> pdb=" O SER A 43 " (cutoff:3.500A) Proline residue: A 47 - end of helix removed outlier: 5.110A pdb=" N LYS A 60 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 66 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 88 removed outlier: 3.921A pdb=" N GLN A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A 78 " --> pdb=" O GLN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 No H-bonds generated for 'chain 'A' and resid 93 through 96' Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 128 through 160 removed outlier: 3.610A pdb=" N ALA A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 3.525A pdb=" N HIS A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 176 through 195 removed outlier: 3.567A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 242 through 269 removed outlier: 4.030A pdb=" N GLU A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'B' and resid 21 through 67 removed outlier: 3.504A pdb=" N VAL B 40 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 46 " --> pdb=" O SER B 43 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 5.111A pdb=" N LYS B 60 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 66 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS B 67 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 88 removed outlier: 3.920A pdb=" N GLN B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 96 No H-bonds generated for 'chain 'B' and resid 93 through 96' Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 128 through 160 removed outlier: 3.610A pdb=" N ALA B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Proline residue: B 143 - end of helix removed outlier: 3.526A pdb=" N HIS B 159 " --> pdb=" O ARG B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 176 through 195 removed outlier: 3.566A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 242 through 269 removed outlier: 4.029A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 280 282 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1274 1.34 - 1.46: 1093 1.46 - 1.58: 2019 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4408 Sorted by residual: bond pdb=" CB TRP B 100 " pdb=" CG TRP B 100 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.63e+00 bond pdb=" CB TRP A 100 " pdb=" CG TRP A 100 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.61e+00 bond pdb=" CG LEU B 115 " pdb=" CD1 LEU B 115 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.92e+00 bond pdb=" CG LEU A 115 " pdb=" CD1 LEU A 115 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.92e+00 bond pdb=" CG LEU A 126 " pdb=" CD1 LEU A 126 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 ... (remaining 4403 not shown) Histogram of bond angle deviations from ideal: 101.38 - 107.97: 146 107.97 - 114.56: 2393 114.56 - 121.16: 2446 121.16 - 127.75: 937 127.75 - 134.34: 48 Bond angle restraints: 5970 Sorted by residual: angle pdb=" CA LYS B 246 " pdb=" CB LYS B 246 " pdb=" CG LYS B 246 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA LYS A 246 " pdb=" CB LYS A 246 " pdb=" CG LYS A 246 " ideal model delta sigma weight residual 114.10 123.58 -9.48 2.00e+00 2.50e-01 2.25e+01 angle pdb=" CB LYS A 246 " pdb=" CG LYS A 246 " pdb=" CD LYS A 246 " ideal model delta sigma weight residual 111.30 120.15 -8.85 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CB LYS B 246 " pdb=" CG LYS B 246 " pdb=" CD LYS B 246 " ideal model delta sigma weight residual 111.30 120.09 -8.79 2.30e+00 1.89e-01 1.46e+01 angle pdb=" CG LYS A 274 " pdb=" CD LYS A 274 " pdb=" CE LYS A 274 " ideal model delta sigma weight residual 111.30 118.11 -6.81 2.30e+00 1.89e-01 8.76e+00 ... (remaining 5965 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.12: 2293 16.12 - 32.24: 168 32.24 - 48.35: 34 48.35 - 64.46: 2 64.46 - 80.58: 10 Dihedral angle restraints: 2507 sinusoidal: 987 harmonic: 1520 Sorted by residual: dihedral pdb=" CA LEU B 223 " pdb=" C LEU B 223 " pdb=" N SER B 224 " pdb=" CA SER B 224 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU A 223 " pdb=" C LEU A 223 " pdb=" N SER A 224 " pdb=" CA SER A 224 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASN B 99 " pdb=" CB ASN B 99 " pdb=" CG ASN B 99 " pdb=" OD1 ASN B 99 " ideal model delta sinusoidal sigma weight residual 120.00 -173.61 -66.39 2 2.00e+01 2.50e-03 1.01e+01 ... (remaining 2504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 428 0.046 - 0.093: 157 0.093 - 0.139: 67 0.139 - 0.185: 14 0.185 - 0.232: 2 Chirality restraints: 668 Sorted by residual: chirality pdb=" CB ILE B 221 " pdb=" CA ILE B 221 " pdb=" CG1 ILE B 221 " pdb=" CG2 ILE B 221 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE A 221 " pdb=" CA ILE A 221 " pdb=" CG1 ILE A 221 " pdb=" CG2 ILE A 221 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LYS B 246 " pdb=" N LYS B 246 " pdb=" C LYS B 246 " pdb=" CB LYS B 246 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 665 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 48 " -0.028 2.00e-02 2.50e+03 2.95e-02 1.74e+01 pdb=" CG TYR A 48 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR A 48 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 48 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 48 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 48 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 48 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 48 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 48 " -0.028 2.00e-02 2.50e+03 2.91e-02 1.70e+01 pdb=" CG TYR B 48 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR B 48 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 48 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 48 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 48 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 48 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 48 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 156 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.29e+00 pdb=" C VAL A 156 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL A 156 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 157 " -0.016 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 1384 2.83 - 3.41: 5313 3.41 - 3.99: 7889 3.99 - 4.56: 11211 4.56 - 5.14: 15919 Nonbonded interactions: 41716 Sorted by model distance: nonbonded pdb=" OD1 ASP A 128 " pdb=" N GLY A 129 " model vdw 2.254 2.520 nonbonded pdb=" OD1 ASP B 128 " pdb=" N GLY B 129 " model vdw 2.254 2.520 nonbonded pdb=" O ASN B 99 " pdb=" ND2 ASN B 99 " model vdw 2.286 2.520 nonbonded pdb=" O ASN A 99 " pdb=" ND2 ASN A 99 " model vdw 2.287 2.520 nonbonded pdb=" OH TYR A 120 " pdb=" OG SER A 222 " model vdw 2.358 2.440 ... (remaining 41711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 281) selection = (chain 'B' and resid 20 through 281) } 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: 0.340 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: 1.850 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.260 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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 : 0.009 0.059 4408 Z= 0.555 Angle : 1.065 9.548 5970 Z= 0.564 Chirality : 0.058 0.232 668 Planarity : 0.006 0.035 728 Dihedral : 12.815 80.576 1532 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.13 % 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: 1.09 (0.37), residues: 520 helix: 1.51 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -2.07 (0.61), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 210 HIS 0.007 0.003 HIS B 159 PHE 0.030 0.004 PHE B 174 TYR 0.072 0.004 TYR A 48 ARG 0.003 0.001 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.506 Fit side-chains REVERT: B 247 ILE cc_start: 0.8402 (tt) cc_final: 0.8197 (tt) outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.1807 time to fit residues: 18.7237 Evaluate side-chains 73 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4408 Z= 0.229 Angle : 0.624 5.855 5970 Z= 0.344 Chirality : 0.040 0.132 668 Planarity : 0.006 0.032 728 Dihedral : 5.295 56.382 602 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.96 % Allowed : 10.00 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.36), residues: 520 helix: 0.94 (0.24), residues: 412 sheet: None (None), residues: 0 loop : -2.41 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 172 HIS 0.005 0.002 HIS B 169 PHE 0.013 0.001 PHE B 133 TYR 0.014 0.002 TYR A 137 ARG 0.002 0.001 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.6445 (tt0) cc_final: 0.6032 (mt0) outliers start: 9 outliers final: 9 residues processed: 94 average time/residue: 0.1696 time to fit residues: 19.9980 Evaluate side-chains 85 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 222 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 47 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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: 0.7096 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4408 Z= 0.161 Angle : 0.529 5.612 5970 Z= 0.291 Chirality : 0.038 0.171 668 Planarity : 0.005 0.033 728 Dihedral : 5.126 58.242 602 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.61 % Allowed : 14.78 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.36), residues: 520 helix: 0.87 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.34 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 210 HIS 0.003 0.001 HIS A 169 PHE 0.021 0.001 PHE A 276 TYR 0.011 0.001 TYR A 137 ARG 0.004 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.517 Fit side-chains REVERT: A 274 LYS cc_start: 0.7330 (pttm) cc_final: 0.6832 (ptpp) REVERT: B 103 ASP cc_start: 0.7445 (p0) cc_final: 0.7223 (p0) outliers start: 12 outliers final: 3 residues processed: 100 average time/residue: 0.1530 time to fit residues: 19.4209 Evaluate side-chains 87 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 266 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 0.0060 chunk 0 optimal weight: 4.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4408 Z= 0.277 Angle : 0.581 5.825 5970 Z= 0.314 Chirality : 0.038 0.128 668 Planarity : 0.005 0.032 728 Dihedral : 5.364 57.947 602 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.48 % Allowed : 16.30 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.37), residues: 520 helix: 0.93 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -2.53 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 210 HIS 0.004 0.001 HIS A 169 PHE 0.012 0.002 PHE B 133 TYR 0.012 0.001 TYR A 245 ARG 0.003 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.516 Fit side-chains REVERT: A 71 SER cc_start: 0.8122 (m) cc_final: 0.7391 (t) REVERT: A 103 ASP cc_start: 0.7540 (p0) cc_final: 0.7270 (p0) REVERT: B 77 GLN cc_start: 0.7903 (pp30) cc_final: 0.7675 (pp30) REVERT: B 103 ASP cc_start: 0.7707 (p0) cc_final: 0.7454 (p0) REVERT: B 274 LYS cc_start: 0.7353 (pttm) cc_final: 0.6839 (ptpp) outliers start: 16 outliers final: 14 residues processed: 97 average time/residue: 0.1937 time to fit residues: 22.9979 Evaluate side-chains 103 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4408 Z= 0.199 Angle : 0.518 5.678 5970 Z= 0.282 Chirality : 0.037 0.123 668 Planarity : 0.005 0.031 728 Dihedral : 5.252 57.921 602 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.26 % Allowed : 18.26 % Favored : 78.48 % 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: 0.35 (0.37), residues: 520 helix: 0.92 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -2.36 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 210 HIS 0.002 0.001 HIS B 67 PHE 0.019 0.001 PHE B 276 TYR 0.009 0.001 TYR B 137 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.494 Fit side-chains REVERT: A 71 SER cc_start: 0.8085 (m) cc_final: 0.7478 (t) REVERT: A 103 ASP cc_start: 0.7533 (p0) cc_final: 0.7233 (p0) REVERT: B 103 ASP cc_start: 0.7636 (p0) cc_final: 0.7313 (p0) REVERT: B 167 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.6211 (m-10) REVERT: B 274 LYS cc_start: 0.7407 (pttm) cc_final: 0.6857 (ptpp) outliers start: 15 outliers final: 11 residues processed: 94 average time/residue: 0.1660 time to fit residues: 19.5325 Evaluate side-chains 99 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 267 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4408 Z= 0.186 Angle : 0.522 8.167 5970 Z= 0.284 Chirality : 0.036 0.120 668 Planarity : 0.005 0.028 728 Dihedral : 5.192 58.164 602 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.26 % Allowed : 19.13 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.37), residues: 520 helix: 0.91 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.40 (0.55), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.002 0.001 HIS B 67 PHE 0.017 0.001 PHE A 133 TYR 0.008 0.001 TYR B 245 ARG 0.005 0.000 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.495 Fit side-chains REVERT: A 103 ASP cc_start: 0.7521 (p0) cc_final: 0.7214 (p0) REVERT: A 239 GLN cc_start: 0.6405 (tt0) cc_final: 0.6140 (mt0) REVERT: B 103 ASP cc_start: 0.7476 (p0) cc_final: 0.7145 (p0) REVERT: B 167 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6721 (m-10) REVERT: B 171 ARG cc_start: 0.6519 (mtm180) cc_final: 0.5714 (mtt180) REVERT: B 274 LYS cc_start: 0.7384 (pttm) cc_final: 0.7135 (pttm) outliers start: 15 outliers final: 11 residues processed: 96 average time/residue: 0.1877 time to fit residues: 22.1422 Evaluate side-chains 99 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 267 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4408 Z= 0.198 Angle : 0.514 5.685 5970 Z= 0.280 Chirality : 0.037 0.125 668 Planarity : 0.005 0.029 728 Dihedral : 5.163 58.057 602 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.48 % Allowed : 19.78 % Favored : 76.74 % 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: 0.38 (0.37), residues: 520 helix: 0.95 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.36 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 100 HIS 0.002 0.001 HIS A 159 PHE 0.018 0.001 PHE B 280 TYR 0.009 0.001 TYR A 245 ARG 0.002 0.000 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.487 Fit side-chains REVERT: A 67 HIS cc_start: 0.6445 (OUTLIER) cc_final: 0.5975 (m-70) REVERT: A 103 ASP cc_start: 0.7492 (p0) cc_final: 0.7190 (p0) REVERT: A 274 LYS cc_start: 0.7320 (pttm) cc_final: 0.6808 (ptpp) REVERT: B 103 ASP cc_start: 0.7430 (p0) cc_final: 0.7098 (p0) REVERT: B 167 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.6198 (m-10) REVERT: B 254 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7737 (tt) REVERT: B 274 LYS cc_start: 0.7411 (pttm) cc_final: 0.7123 (pttm) outliers start: 16 outliers final: 11 residues processed: 98 average time/residue: 0.1857 time to fit residues: 22.4716 Evaluate side-chains 99 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 266 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.0670 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.0570 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4408 Z= 0.171 Angle : 0.546 9.489 5970 Z= 0.294 Chirality : 0.037 0.121 668 Planarity : 0.005 0.023 728 Dihedral : 5.113 58.791 602 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.26 % Allowed : 21.30 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.37), residues: 520 helix: 0.95 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -2.35 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 210 HIS 0.002 0.000 HIS B 67 PHE 0.020 0.001 PHE B 280 TYR 0.009 0.001 TYR B 48 ARG 0.004 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.443 Fit side-chains REVERT: A 67 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.5979 (m-70) REVERT: A 103 ASP cc_start: 0.7358 (p0) cc_final: 0.7057 (p0) REVERT: A 279 MET cc_start: 0.6712 (ppp) cc_final: 0.5242 (ttp) REVERT: B 103 ASP cc_start: 0.7414 (p0) cc_final: 0.7101 (p0) REVERT: B 274 LYS cc_start: 0.7413 (pttm) cc_final: 0.7098 (pttm) outliers start: 15 outliers final: 10 residues processed: 97 average time/residue: 0.1662 time to fit residues: 20.2472 Evaluate side-chains 97 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 267 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4408 Z= 0.236 Angle : 0.581 7.492 5970 Z= 0.308 Chirality : 0.038 0.123 668 Planarity : 0.006 0.076 728 Dihedral : 5.201 57.923 602 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.26 % Allowed : 21.30 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.37), residues: 520 helix: 0.92 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -2.42 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 100 HIS 0.002 0.001 HIS B 169 PHE 0.019 0.001 PHE B 280 TYR 0.009 0.001 TYR B 245 ARG 0.008 0.001 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.521 Fit side-chains REVERT: A 67 HIS cc_start: 0.6338 (OUTLIER) cc_final: 0.6013 (m-70) REVERT: A 103 ASP cc_start: 0.7561 (p0) cc_final: 0.7216 (p0) REVERT: A 254 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7722 (tt) REVERT: B 103 ASP cc_start: 0.7433 (p0) cc_final: 0.7103 (p0) REVERT: B 274 LYS cc_start: 0.7463 (pttm) cc_final: 0.7138 (pttm) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.1706 time to fit residues: 20.1963 Evaluate side-chains 96 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4408 Z= 0.168 Angle : 0.544 7.485 5970 Z= 0.293 Chirality : 0.036 0.124 668 Planarity : 0.005 0.064 728 Dihedral : 5.092 58.568 602 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.04 % Allowed : 21.52 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.37), residues: 520 helix: 0.87 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -2.59 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 210 HIS 0.002 0.001 HIS B 169 PHE 0.021 0.001 PHE B 280 TYR 0.008 0.001 TYR A 137 ARG 0.007 0.001 ARG A 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.540 Fit side-chains REVERT: A 67 HIS cc_start: 0.6094 (OUTLIER) cc_final: 0.5816 (m-70) REVERT: A 103 ASP cc_start: 0.7379 (p0) cc_final: 0.7090 (p0) REVERT: A 274 LYS cc_start: 0.7512 (pttm) cc_final: 0.7076 (ptpp) REVERT: A 279 MET cc_start: 0.6633 (ppp) cc_final: 0.5219 (ttp) REVERT: B 103 ASP cc_start: 0.7350 (p0) cc_final: 0.7034 (p0) REVERT: B 274 LYS cc_start: 0.7402 (pttm) cc_final: 0.7077 (pttm) REVERT: B 279 MET cc_start: 0.6845 (ppp) cc_final: 0.5140 (ttp) outliers start: 14 outliers final: 12 residues processed: 91 average time/residue: 0.1626 time to fit residues: 18.8347 Evaluate side-chains 91 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.0270 chunk 36 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.0030 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 overall best weight: 0.2546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.129154 restraints weight = 6030.092| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.54 r_work: 0.3478 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.180 4408 Z= 0.456 Angle : 1.177 59.200 5970 Z= 0.716 Chirality : 0.048 0.813 668 Planarity : 0.006 0.060 728 Dihedral : 5.333 58.572 602 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.83 % Allowed : 22.17 % Favored : 75.00 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.21 (0.37), residues: 520 helix: 0.87 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -2.58 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 210 HIS 0.001 0.001 HIS B 169 PHE 0.019 0.001 PHE B 280 TYR 0.007 0.001 TYR A 137 ARG 0.006 0.001 ARG B 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1334.88 seconds wall clock time: 24 minutes 47.20 seconds (1487.20 seconds total)