Starting phenix.real_space_refine on Sun Mar 10 21:49:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru6_24698/03_2024/7ru6_24698.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru6_24698/03_2024/7ru6_24698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru6_24698/03_2024/7ru6_24698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru6_24698/03_2024/7ru6_24698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru6_24698/03_2024/7ru6_24698.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru6_24698/03_2024/7ru6_24698.pdb" } resolution = 4.4 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 19 5.16 5 C 1815 2.51 5 N 413 2.21 5 O 454 1.98 5 H 2725 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5426 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5148 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain breaks: 4 Chain: "L" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 278 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Time building chain proxies: 3.14, per 1000 atoms: 0.58 Number of scatterers: 5426 At special positions: 0 Unit cell: (62.304, 86.966, 73.986, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 O 454 8.00 N 413 7.00 C 1815 6.00 H 2725 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 4.42 Conformation dependent library (CDL) restraints added in 656.6 milliseconds 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 630 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 86.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 34 through 57 Processing helix chain 'A' and resid 58 through 67 removed outlier: 3.635A pdb=" N GLU A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 116 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 133 through 151 removed outlier: 3.509A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 197 removed outlier: 3.650A pdb=" N SER A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 229 removed outlier: 3.558A pdb=" N TRP A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.567A pdb=" N HIS A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 289 removed outlier: 3.688A pdb=" N SER A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 404 through 423 Processing helix chain 'A' and resid 440 through 463 Processing helix chain 'L' and resid 113 through 117 removed outlier: 3.569A pdb=" N ARG L 117 " --> pdb=" O GLY L 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 105 through 107 220 hydrogen bonds defined for protein. 645 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: 1.99 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2718 1.03 - 1.23: 7 1.23 - 1.42: 1231 1.42 - 1.61: 1518 1.61 - 1.81: 31 Bond restraints: 5505 Sorted by residual: bond pdb=" CB TRP A 284 " pdb=" CG TRP A 284 " ideal model delta sigma weight residual 1.498 1.536 -0.038 3.10e-02 1.04e+03 1.52e+00 bond pdb=" CA TYR L 109 " pdb=" C TYR L 109 " ideal model delta sigma weight residual 1.522 1.502 0.020 1.72e-02 3.38e+03 1.29e+00 bond pdb=" N GLY A 132 " pdb=" CA GLY A 132 " ideal model delta sigma weight residual 1.442 1.450 -0.008 7.70e-03 1.69e+04 1.10e+00 bond pdb=" CB MET A 411 " pdb=" CG MET A 411 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" C TRP L 108 " pdb=" N TYR L 109 " ideal model delta sigma weight residual 1.333 1.319 0.014 1.56e-02 4.11e+03 8.31e-01 ... (remaining 5500 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.65: 78 106.65 - 113.49: 6274 113.49 - 120.33: 2015 120.33 - 127.17: 1501 127.17 - 134.01: 41 Bond angle restraints: 9909 Sorted by residual: angle pdb=" CB MET A 411 " pdb=" CG MET A 411 " pdb=" SD MET A 411 " ideal model delta sigma weight residual 112.70 120.70 -8.00 3.00e+00 1.11e-01 7.11e+00 angle pdb=" CA MET A 411 " pdb=" CB MET A 411 " pdb=" CG MET A 411 " ideal model delta sigma weight residual 114.10 119.04 -4.94 2.00e+00 2.50e-01 6.10e+00 angle pdb=" CA TRP A 284 " pdb=" CB TRP A 284 " pdb=" CG TRP A 284 " ideal model delta sigma weight residual 113.60 118.28 -4.68 1.90e+00 2.77e-01 6.08e+00 angle pdb=" CA MET A 105 " pdb=" CB MET A 105 " pdb=" CG MET A 105 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.46e+00 angle pdb=" C ILE A 55 " pdb=" N MET A 56 " pdb=" CA MET A 56 " ideal model delta sigma weight residual 120.72 117.40 3.32 1.67e+00 3.59e-01 3.95e+00 ... (remaining 9904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 2328 16.40 - 32.81: 182 32.81 - 49.21: 70 49.21 - 65.62: 19 65.62 - 82.02: 3 Dihedral angle restraints: 2602 sinusoidal: 1320 harmonic: 1282 Sorted by residual: dihedral pdb=" N LEU A 412 " pdb=" CA LEU A 412 " pdb=" CB LEU A 412 " pdb=" CG LEU A 412 " ideal model delta sinusoidal sigma weight residual -60.00 -119.36 59.36 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 61 " pdb=" CG MET A 61 " pdb=" SD MET A 61 " pdb=" CE MET A 61 " ideal model delta sinusoidal sigma weight residual 180.00 121.39 58.61 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB GLU A 62 " pdb=" CG GLU A 62 " pdb=" CD GLU A 62 " pdb=" OE1 GLU A 62 " ideal model delta sinusoidal sigma weight residual 0.00 -82.02 82.02 1 3.00e+01 1.11e-03 9.19e+00 ... (remaining 2599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 276 0.026 - 0.052: 90 0.052 - 0.078: 45 0.078 - 0.104: 13 0.104 - 0.131: 3 Chirality restraints: 427 Sorted by residual: chirality pdb=" CA ILE A 151 " pdb=" N ILE A 151 " pdb=" C ILE A 151 " pdb=" CB ILE A 151 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA PRO A 265 " pdb=" N PRO A 265 " pdb=" C PRO A 265 " pdb=" CB PRO A 265 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA PRO A 441 " pdb=" N PRO A 441 " pdb=" C PRO A 441 " pdb=" CB PRO A 441 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 424 not shown) Planarity restraints: 757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 113 " -0.004 2.00e-02 2.50e+03 5.72e-03 9.81e-01 pdb=" CG TYR L 113 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR L 113 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR L 113 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR L 113 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR L 113 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR L 113 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 113 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR L 113 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR L 113 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR L 113 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR L 113 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 290 " -0.016 5.00e-02 4.00e+02 2.36e-02 8.94e-01 pdb=" N PRO A 291 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 281 " 0.010 2.00e-02 2.50e+03 5.03e-03 7.60e-01 pdb=" CG TYR A 281 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 281 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 281 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 281 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR A 281 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 281 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 281 " 0.001 2.00e-02 2.50e+03 ... (remaining 754 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 294 2.19 - 2.79: 10824 2.79 - 3.39: 15567 3.39 - 4.00: 18460 4.00 - 4.60: 29146 Nonbonded interactions: 74291 Sorted by model distance: nonbonded pdb=" OG SER A 285 " pdb=" HZ3 LYS A 446 " model vdw 1.583 1.850 nonbonded pdb=" O GLU A 290 " pdb="HD22 ASN A 296 " model vdw 1.632 1.850 nonbonded pdb=" O CYS A 413 " pdb=" HG SER A 416 " model vdw 1.647 1.850 nonbonded pdb=" OD1 ASP A 124 " pdb=" H ARG A 126 " model vdw 1.669 1.850 nonbonded pdb=" OE2 GLU A 195 " pdb=" H GLY L 114 " model vdw 1.682 1.850 ... (remaining 74286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.090 Extract box with map and model: 1.900 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.590 Find NCS groups from input model: 0.090 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 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 : 0.003 0.038 2780 Z= 0.218 Angle : 0.587 7.998 3774 Z= 0.313 Chirality : 0.035 0.131 427 Planarity : 0.003 0.031 440 Dihedral : 15.250 82.022 950 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.00 % Allowed : 22.64 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.46), residues: 319 helix: 2.60 (0.30), residues: 261 sheet: None (None), residues: 0 loop : -0.42 (0.86), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 440 HIS 0.005 0.001 HIS A 130 PHE 0.011 0.001 PHE A 110 TYR 0.015 0.002 TYR L 113 ARG 0.001 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.3046 time to fit residues: 21.5880 Evaluate side-chains 56 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2780 Z= 0.198 Angle : 0.482 5.064 3774 Z= 0.274 Chirality : 0.034 0.116 427 Planarity : 0.003 0.026 440 Dihedral : 3.490 13.464 359 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.45), residues: 319 helix: 2.73 (0.29), residues: 262 sheet: None (None), residues: 0 loop : -0.20 (0.88), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 284 HIS 0.004 0.001 HIS A 130 PHE 0.011 0.001 PHE A 112 TYR 0.021 0.001 TYR A 281 ARG 0.001 0.000 ARG L 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8649 (t80) cc_final: 0.8430 (t80) REVERT: A 142 ILE cc_start: 0.7054 (mm) cc_final: 0.6714 (mm) REVERT: A 188 GLU cc_start: 0.8659 (tt0) cc_final: 0.7859 (mt-10) REVERT: A 226 THR cc_start: 0.7667 (m) cc_final: 0.7464 (m) REVERT: A 411 MET cc_start: 0.8283 (tmm) cc_final: 0.7807 (tmm) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3565 time to fit residues: 30.0716 Evaluate side-chains 60 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.0170 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2780 Z= 0.171 Angle : 0.472 4.794 3774 Z= 0.266 Chirality : 0.033 0.117 427 Planarity : 0.003 0.025 440 Dihedral : 3.430 14.497 359 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.34 % Allowed : 2.36 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.72 (0.44), residues: 319 helix: 2.93 (0.29), residues: 262 sheet: None (None), residues: 0 loop : 0.06 (0.87), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 108 HIS 0.007 0.001 HIS A 130 PHE 0.012 0.001 PHE A 112 TYR 0.021 0.002 TYR A 281 ARG 0.001 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: A 411 MET cc_start: 0.8166 (tmm) cc_final: 0.7625 (tmm) REVERT: A 453 CYS cc_start: 0.9265 (t) cc_final: 0.9060 (t) REVERT: L 107 SER cc_start: 0.8994 (m) cc_final: 0.8133 (p) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.3210 time to fit residues: 26.6950 Evaluate side-chains 59 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.6788 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2780 Z= 0.226 Angle : 0.500 5.058 3774 Z= 0.283 Chirality : 0.034 0.124 427 Planarity : 0.003 0.025 440 Dihedral : 3.531 15.227 359 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.43), residues: 319 helix: 2.85 (0.28), residues: 264 sheet: None (None), residues: 0 loop : -0.07 (0.88), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 202 HIS 0.005 0.002 HIS A 130 PHE 0.011 0.001 PHE A 112 TYR 0.022 0.002 TYR A 225 ARG 0.002 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8716 (tt0) cc_final: 0.8144 (tm-30) REVERT: A 411 MET cc_start: 0.8196 (tmm) cc_final: 0.7671 (tmm) REVERT: A 453 CYS cc_start: 0.9242 (t) cc_final: 0.9004 (t) REVERT: L 106 TYR cc_start: 0.9134 (m-80) cc_final: 0.8889 (m-80) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2924 time to fit residues: 23.2410 Evaluate side-chains 54 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2780 Z= 0.188 Angle : 0.475 5.001 3774 Z= 0.265 Chirality : 0.034 0.117 427 Planarity : 0.003 0.026 440 Dihedral : 3.442 14.251 359 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.44), residues: 319 helix: 2.94 (0.28), residues: 264 sheet: None (None), residues: 0 loop : -0.01 (0.87), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 190 HIS 0.004 0.001 HIS A 130 PHE 0.005 0.001 PHE L 102 TYR 0.022 0.001 TYR A 281 ARG 0.001 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.8237 (tmm) cc_final: 0.7685 (tmm) REVERT: A 453 CYS cc_start: 0.9155 (t) cc_final: 0.8892 (t) REVERT: L 106 TYR cc_start: 0.9133 (m-80) cc_final: 0.8864 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.3089 time to fit residues: 24.5901 Evaluate side-chains 53 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 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 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 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 : 0.003 0.017 2780 Z= 0.174 Angle : 0.469 4.779 3774 Z= 0.259 Chirality : 0.034 0.114 427 Planarity : 0.003 0.026 440 Dihedral : 3.366 15.346 359 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.44), residues: 319 helix: 3.06 (0.28), residues: 264 sheet: None (None), residues: 0 loop : 0.14 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 115 HIS 0.003 0.001 HIS A 409 PHE 0.011 0.001 PHE A 112 TYR 0.019 0.001 TYR A 281 ARG 0.001 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.8144 (tmm) cc_final: 0.7590 (tmm) REVERT: A 453 CYS cc_start: 0.9140 (t) cc_final: 0.8730 (t) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2897 time to fit residues: 23.1208 Evaluate side-chains 56 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.0370 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2780 Z= 0.135 Angle : 0.438 5.131 3774 Z= 0.237 Chirality : 0.033 0.107 427 Planarity : 0.003 0.028 440 Dihedral : 3.285 14.950 359 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: 4.32 (0.44), residues: 319 helix: 3.31 (0.29), residues: 264 sheet: None (None), residues: 0 loop : 0.33 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 115 HIS 0.002 0.001 HIS A 409 PHE 0.010 0.001 PHE A 112 TYR 0.018 0.001 TYR A 281 ARG 0.001 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.6844 (mm) cc_final: 0.6641 (mm) REVERT: A 411 MET cc_start: 0.8110 (tmm) cc_final: 0.7555 (tmm) REVERT: A 453 CYS cc_start: 0.9019 (t) cc_final: 0.8778 (t) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3083 time to fit residues: 24.3342 Evaluate side-chains 57 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2780 Z= 0.222 Angle : 0.522 4.898 3774 Z= 0.289 Chirality : 0.035 0.125 427 Planarity : 0.003 0.025 440 Dihedral : 3.423 16.198 359 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.44), residues: 319 helix: 3.00 (0.28), residues: 264 sheet: None (None), residues: 0 loop : 0.07 (0.86), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 115 HIS 0.003 0.001 HIS A 130 PHE 0.011 0.001 PHE A 112 TYR 0.021 0.002 TYR A 281 ARG 0.003 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ILE cc_start: 0.7827 (pt) cc_final: 0.7623 (pt) REVERT: A 188 GLU cc_start: 0.8681 (tt0) cc_final: 0.8128 (tm-30) REVERT: A 411 MET cc_start: 0.8198 (tmm) cc_final: 0.7666 (tmm) REVERT: A 453 CYS cc_start: 0.9066 (t) cc_final: 0.8685 (t) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3458 time to fit residues: 27.2606 Evaluate side-chains 55 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.0030 chunk 19 optimal weight: 0.5980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2780 Z= 0.145 Angle : 0.443 5.129 3774 Z= 0.242 Chirality : 0.033 0.110 427 Planarity : 0.003 0.027 440 Dihedral : 3.314 15.570 359 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 4.14 (0.44), residues: 319 helix: 3.23 (0.29), residues: 263 sheet: None (None), residues: 0 loop : 0.08 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 115 HIS 0.002 0.001 HIS A 130 PHE 0.008 0.001 PHE A 209 TYR 0.017 0.001 TYR A 281 ARG 0.002 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.6896 (mm) cc_final: 0.6586 (mm) REVERT: A 411 MET cc_start: 0.8111 (tmm) cc_final: 0.7555 (tmm) REVERT: A 453 CYS cc_start: 0.9017 (t) cc_final: 0.8687 (t) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3207 time to fit residues: 24.6744 Evaluate side-chains 55 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 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 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2780 Z= 0.202 Angle : 0.491 5.012 3774 Z= 0.275 Chirality : 0.034 0.121 427 Planarity : 0.003 0.026 440 Dihedral : 3.429 16.555 359 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.44), residues: 319 helix: 2.97 (0.28), residues: 264 sheet: None (None), residues: 0 loop : 0.02 (0.87), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 115 HIS 0.003 0.001 HIS A 409 PHE 0.015 0.001 PHE A 112 TYR 0.020 0.002 TYR A 281 ARG 0.003 0.001 ARG A 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.8135 (tmm) cc_final: 0.7568 (tmm) REVERT: A 453 CYS cc_start: 0.9041 (t) cc_final: 0.8692 (t) REVERT: L 106 TYR cc_start: 0.9216 (m-80) cc_final: 0.9001 (m-80) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3055 time to fit residues: 23.6910 Evaluate side-chains 54 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.131365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110464 restraints weight = 15285.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114500 restraints weight = 7383.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.116940 restraints weight = 4494.977| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2780 Z= 0.170 Angle : 0.491 7.524 3774 Z= 0.261 Chirality : 0.034 0.113 427 Planarity : 0.003 0.026 440 Dihedral : 3.383 16.133 359 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.44), residues: 319 helix: 3.06 (0.29), residues: 264 sheet: None (None), residues: 0 loop : 0.00 (0.87), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 115 HIS 0.002 0.001 HIS A 130 PHE 0.013 0.001 PHE A 112 TYR 0.016 0.001 TYR A 281 ARG 0.002 0.000 ARG A 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2280.13 seconds wall clock time: 40 minutes 53.63 seconds (2453.63 seconds total)