Starting phenix.real_space_refine on Mon Sep 23 18:27:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/09_2024/7sk1_25169.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/09_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_25169/09_2024/7sk1_25169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/09_2024/7sk1_25169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/09_2024/7sk1_25169.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/09_2024/7sk1_25169.cif" } 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. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 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: 3.35, per 1000 atoms: 0.78 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 446.7 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... Secondary structure from input PDB file: 22 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 21 through 68 removed outlier: 3.876A pdb=" N PHE A 25 " --> pdb=" O TRP A 21 " (cutoff:3.500A) Proline residue: A 47 - end of helix removed outlier: 4.441A pdb=" N ARG A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 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 92 through 97 removed outlier: 3.847A pdb=" N SER A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 127 through 161 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 161 through 172 removed outlier: 3.729A pdb=" N TRP A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 196 removed outlier: 3.567A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 207 Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 241 through 270 removed outlier: 4.030A pdb=" N GLU A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'B' and resid 21 through 68 removed outlier: 3.875A pdb=" N PHE B 25 " --> pdb=" O TRP B 21 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 4.442A pdb=" N ARG B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 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 92 through 97 removed outlier: 3.847A pdb=" N SER B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 127 through 161 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 161 through 172 removed outlier: 3.730A pdb=" N TRP B 172 " --> pdb=" O PHE B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 196 removed outlier: 3.566A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 207 Processing helix chain 'B' and resid 211 through 224 Processing helix chain 'B' and resid 241 through 270 removed outlier: 4.029A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 324 hydrogen bonds defined for protein. 972 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: 1.11 Time building geometry restraints manager: 1.27 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: 0.00 - 1.91: 5562 1.91 - 3.82: 335 3.82 - 5.73: 49 5.73 - 7.64: 16 7.64 - 9.55: 8 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: 1366 2.83 - 3.41: 5281 3.41 - 3.99: 7840 3.99 - 4.56: 11142 4.56 - 5.14: 15919 Nonbonded interactions: 41548 Sorted by model distance: nonbonded pdb=" OD1 ASP A 128 " pdb=" N GLY A 129 " model vdw 2.254 3.120 nonbonded pdb=" OD1 ASP B 128 " pdb=" N GLY B 129 " model vdw 2.254 3.120 nonbonded pdb=" O ASN B 99 " pdb=" ND2 ASN B 99 " model vdw 2.286 3.120 nonbonded pdb=" O ASN A 99 " pdb=" ND2 ASN A 99 " model vdw 2.287 3.120 nonbonded pdb=" OH TYR A 120 " pdb=" OG SER A 222 " model vdw 2.358 3.040 ... (remaining 41543 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' 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: 0.490 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.550 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- 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= 0.550 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 : 0.455 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: 0.1792 time to fit residues: 18.5197 Evaluate side-chains 73 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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: 0.6980 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7102 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4408 Z= 0.259 Angle : 0.661 5.860 5970 Z= 0.358 Chirality : 0.042 0.174 668 Planarity : 0.004 0.031 728 Dihedral : 5.108 56.731 602 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.30 % Allowed : 10.00 % Favored : 88.70 % 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: 520 helix: 1.60 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.28 (0.66), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.006 0.002 HIS A 169 PHE 0.024 0.002 PHE A 280 TYR 0.014 0.002 TYR A 137 ARG 0.002 0.001 ARG A 81 *********************** 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: 6 poor density : 93 time to evaluate : 0.368 Fit side-chains REVERT: A 239 GLN cc_start: 0.6458 (tt0) cc_final: 0.6041 (mt0) REVERT: A 243 GLU cc_start: 0.6773 (pm20) cc_final: 0.6493 (pt0) REVERT: B 102 TRP cc_start: 0.7928 (m100) cc_final: 0.7724 (m100) REVERT: B 243 GLU cc_start: 0.6913 (pm20) cc_final: 0.6575 (pt0) outliers start: 6 outliers final: 4 residues processed: 99 average time/residue: 0.1842 time to fit residues: 22.2995 Evaluate side-chains 80 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 79 LEU 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: 0.5980 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 16 optimal weight: 0.0470 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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: 0.7086 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4408 Z= 0.172 Angle : 0.590 6.554 5970 Z= 0.316 Chirality : 0.040 0.174 668 Planarity : 0.004 0.038 728 Dihedral : 4.950 57.520 602 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.70 % Allowed : 12.83 % Favored : 83.48 % 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: 1.65 (0.37), residues: 520 helix: 1.84 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.32 (0.65), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 210 HIS 0.005 0.001 HIS A 169 PHE 0.020 0.002 PHE B 280 TYR 0.012 0.001 TYR B 137 ARG 0.006 0.001 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 116 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.460 Fit side-chains REVERT: A 279 MET cc_start: 0.6527 (ppp) cc_final: 0.5346 (ttp) REVERT: B 243 GLU cc_start: 0.7008 (pm20) cc_final: 0.6657 (pt0) REVERT: B 255 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7984 (mt) REVERT: B 273 LEU cc_start: 0.8528 (tp) cc_final: 0.8245 (mm) outliers start: 17 outliers final: 8 residues processed: 113 average time/residue: 0.1608 time to fit residues: 22.7219 Evaluate side-chains 86 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 255 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7106 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4408 Z= 0.182 Angle : 0.573 6.704 5970 Z= 0.302 Chirality : 0.038 0.141 668 Planarity : 0.004 0.036 728 Dihedral : 4.922 58.718 602 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.83 % Allowed : 18.70 % 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: 1.83 (0.37), residues: 520 helix: 2.00 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.43 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 210 HIS 0.004 0.001 HIS A 169 PHE 0.019 0.002 PHE B 276 TYR 0.010 0.001 TYR B 88 ARG 0.005 0.000 ARG A 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 98 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 67 HIS cc_start: 0.6885 (OUTLIER) cc_final: 0.6556 (m-70) REVERT: A 71 SER cc_start: 0.8058 (m) cc_final: 0.7425 (t) REVERT: A 174 PHE cc_start: 0.6836 (p90) cc_final: 0.6613 (p90) REVERT: A 279 MET cc_start: 0.6249 (ppp) cc_final: 0.5201 (ttp) REVERT: B 279 MET cc_start: 0.6404 (ppp) cc_final: 0.5128 (ttp) outliers start: 13 outliers final: 6 residues processed: 96 average time/residue: 0.2262 time to fit residues: 26.3378 Evaluate side-chains 84 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 222 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7160 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4408 Z= 0.235 Angle : 0.609 8.545 5970 Z= 0.322 Chirality : 0.040 0.146 668 Planarity : 0.004 0.042 728 Dihedral : 5.042 58.271 602 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % 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: 1.84 (0.37), residues: 520 helix: 1.98 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.31 (0.65), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 210 HIS 0.003 0.001 HIS A 169 PHE 0.022 0.002 PHE B 220 TYR 0.011 0.001 TYR A 88 ARG 0.007 0.001 ARG B 155 *********************** 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 99 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 71 SER cc_start: 0.8103 (m) cc_final: 0.7491 (t) REVERT: A 279 MET cc_start: 0.5984 (ppp) cc_final: 0.5031 (ttp) REVERT: A 280 PHE cc_start: 0.8043 (t80) cc_final: 0.7806 (t80) REVERT: B 77 GLN cc_start: 0.7871 (pp30) cc_final: 0.7643 (pp30) REVERT: B 279 MET cc_start: 0.6276 (ppp) cc_final: 0.5061 (ttp) REVERT: B 280 PHE cc_start: 0.7829 (t80) cc_final: 0.7585 (t80) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.1738 time to fit residues: 20.0942 Evaluate side-chains 88 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 158 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 273 LEU 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: 0.6980 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7158 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4408 Z= 0.207 Angle : 0.586 6.515 5970 Z= 0.311 Chirality : 0.039 0.133 668 Planarity : 0.004 0.046 728 Dihedral : 5.005 58.281 602 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.70 % Allowed : 20.65 % Favored : 75.65 % 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: 1.82 (0.37), residues: 520 helix: 1.98 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.37 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 210 HIS 0.003 0.001 HIS B 271 PHE 0.021 0.002 PHE A 276 TYR 0.022 0.002 TYR A 88 ARG 0.006 0.001 ARG A 155 *********************** 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 104 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 163 ARG cc_start: 0.5733 (ttt180) cc_final: 0.5265 (ttt180) REVERT: A 167 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.6083 (m-10) REVERT: A 239 GLN cc_start: 0.6324 (tt0) cc_final: 0.6063 (mt0) REVERT: A 279 MET cc_start: 0.5772 (ppp) cc_final: 0.5030 (ttp) REVERT: A 280 PHE cc_start: 0.8019 (t80) cc_final: 0.7778 (t80) REVERT: B 77 GLN cc_start: 0.7922 (pp30) cc_final: 0.7656 (pp30) REVERT: B 279 MET cc_start: 0.5973 (ppp) cc_final: 0.4852 (ttp) REVERT: B 280 PHE cc_start: 0.7829 (t80) cc_final: 0.7535 (t80) outliers start: 17 outliers final: 12 residues processed: 99 average time/residue: 0.1762 time to fit residues: 21.8560 Evaluate side-chains 92 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7156 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4408 Z= 0.190 Angle : 0.588 6.997 5970 Z= 0.309 Chirality : 0.038 0.130 668 Planarity : 0.004 0.051 728 Dihedral : 4.977 58.500 602 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.04 % Allowed : 22.17 % Favored : 74.78 % 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: 1.84 (0.37), residues: 520 helix: 1.99 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.37 (0.64), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 100 HIS 0.002 0.001 HIS B 169 PHE 0.028 0.002 PHE B 276 TYR 0.015 0.001 TYR A 88 ARG 0.006 0.001 ARG A 155 *********************** 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 94 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 163 ARG cc_start: 0.5720 (ttt180) cc_final: 0.5256 (ttt180) REVERT: A 167 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6167 (m-10) REVERT: A 239 GLN cc_start: 0.6384 (tt0) cc_final: 0.6071 (mt0) REVERT: A 279 MET cc_start: 0.5642 (ppp) cc_final: 0.4936 (ttp) REVERT: B 66 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: B 77 GLN cc_start: 0.7874 (pp30) cc_final: 0.7610 (pp30) REVERT: B 103 ASP cc_start: 0.8170 (p0) cc_final: 0.7930 (p0) REVERT: B 279 MET cc_start: 0.5963 (ppp) cc_final: 0.4830 (ttp) REVERT: B 280 PHE cc_start: 0.7811 (t80) cc_final: 0.7552 (t80) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.1805 time to fit residues: 20.0681 Evaluate side-chains 90 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7149 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4408 Z= 0.180 Angle : 0.569 6.341 5970 Z= 0.304 Chirality : 0.038 0.128 668 Planarity : 0.004 0.049 728 Dihedral : 4.934 58.807 602 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.13 % Allowed : 22.17 % Favored : 73.70 % 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: 1.84 (0.37), residues: 520 helix: 2.00 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.40 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 210 HIS 0.002 0.001 HIS B 271 PHE 0.032 0.002 PHE B 276 TYR 0.016 0.001 TYR A 88 ARG 0.007 0.001 ARG A 155 *********************** 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 101 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8084 (p0) cc_final: 0.7877 (p0) REVERT: A 167 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6134 (m-10) REVERT: A 239 GLN cc_start: 0.6305 (tt0) cc_final: 0.6050 (mt0) REVERT: A 254 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7778 (tt) REVERT: A 279 MET cc_start: 0.5566 (ppp) cc_final: 0.4916 (ttp) REVERT: B 77 GLN cc_start: 0.7835 (pp30) cc_final: 0.7604 (pp30) REVERT: B 103 ASP cc_start: 0.8037 (p0) cc_final: 0.7827 (p0) REVERT: B 279 MET cc_start: 0.5832 (ppp) cc_final: 0.4830 (ttp) outliers start: 19 outliers final: 13 residues processed: 94 average time/residue: 0.1665 time to fit residues: 19.5341 Evaluate side-chains 95 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 0.0370 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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: 0.7158 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4408 Z= 0.201 Angle : 0.582 6.188 5970 Z= 0.313 Chirality : 0.039 0.129 668 Planarity : 0.004 0.058 728 Dihedral : 4.945 58.795 602 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.35 % Allowed : 22.39 % Favored : 73.26 % 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: 1.82 (0.37), residues: 520 helix: 1.97 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.33 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 100 HIS 0.004 0.001 HIS A 67 PHE 0.020 0.001 PHE A 220 TYR 0.015 0.001 TYR A 88 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 97 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8105 (p0) cc_final: 0.7894 (p0) REVERT: A 167 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.6125 (m-10) REVERT: A 239 GLN cc_start: 0.6376 (tt0) cc_final: 0.6084 (mt0) REVERT: A 254 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7756 (tt) REVERT: A 279 MET cc_start: 0.5581 (ppp) cc_final: 0.4950 (ttp) REVERT: B 77 GLN cc_start: 0.7847 (pp30) cc_final: 0.7611 (pp30) REVERT: B 103 ASP cc_start: 0.8080 (p0) cc_final: 0.7876 (p0) REVERT: B 279 MET cc_start: 0.5755 (ppp) cc_final: 0.4815 (ttp) outliers start: 20 outliers final: 14 residues processed: 92 average time/residue: 0.1588 time to fit residues: 18.4594 Evaluate side-chains 91 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7144 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4408 Z= 0.176 Angle : 0.590 6.922 5970 Z= 0.318 Chirality : 0.038 0.127 668 Planarity : 0.004 0.034 728 Dihedral : 4.909 59.091 602 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.26 % Allowed : 23.91 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.37), residues: 520 helix: 1.93 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.45 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 100 HIS 0.003 0.001 HIS A 67 PHE 0.024 0.002 PHE B 220 TYR 0.015 0.001 TYR A 88 ARG 0.005 0.000 ARG B 57 ********************** 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 94 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.501 Fit side-chains REVERT: A 103 ASP cc_start: 0.8105 (p0) cc_final: 0.7898 (p0) REVERT: A 167 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6156 (m-10) REVERT: A 239 GLN cc_start: 0.6390 (tt0) cc_final: 0.6119 (mt0) REVERT: A 279 MET cc_start: 0.5579 (ppp) cc_final: 0.4945 (ttp) REVERT: B 77 GLN cc_start: 0.7826 (pp30) cc_final: 0.7589 (pp30) REVERT: B 279 MET cc_start: 0.5795 (ppp) cc_final: 0.4876 (ttp) outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 0.1743 time to fit residues: 19.6977 Evaluate side-chains 86 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3852 r_free = 0.3852 target = 0.152771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129200 restraints weight = 6115.331| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.61 r_work: 0.3475 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4408 Z= 0.179 Angle : 0.614 6.863 5970 Z= 0.330 Chirality : 0.038 0.127 668 Planarity : 0.004 0.032 728 Dihedral : 4.875 59.309 602 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.26 % Allowed : 24.13 % Favored : 72.61 % 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: 1.73 (0.37), residues: 520 helix: 1.92 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.38 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 210 HIS 0.002 0.001 HIS A 67 PHE 0.033 0.001 PHE B 144 TYR 0.014 0.001 TYR A 88 ARG 0.004 0.000 ARG B 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1235.10 seconds wall clock time: 22 minutes 58.08 seconds (1378.08 seconds total)