Starting phenix.real_space_refine on Tue Feb 13 07:58:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/02_2024/7y7z_33675_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/02_2024/7y7z_33675.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/02_2024/7y7z_33675_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/02_2024/7y7z_33675_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/02_2024/7y7z_33675_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/02_2024/7y7z_33675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/02_2024/7y7z_33675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/02_2024/7y7z_33675_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/02_2024/7y7z_33675_updated.pdb" } resolution = 3.2 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= 0.002 sd= 0.130 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 36 5.16 5 Cl 1 4.86 5 C 2876 2.51 5 N 661 2.21 5 O 729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4303 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4303 Unusual residues: {' CL': 1, 'NAG': 3, 'TGI': 1} Classifications: {'peptide': 532, 'undetermined': 5} Link IDs: {'PTRANS': 23, 'TRANS': 508, None: 5} Not linked: pdbres="PRO A 580 " pdbres="TGI A 701 " Not linked: pdbres="TGI A 701 " pdbres="NAG A 702 " Not linked: pdbres="NAG A 702 " pdbres="NAG A 703 " Not linked: pdbres="NAG A 703 " pdbres="NAG A 704 " Not linked: pdbres="NAG A 704 " pdbres=" CL A 705 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.98, per 1000 atoms: 0.69 Number of scatterers: 4303 At special positions: 0 Unit cell: (71.445, 74.6925, 96.3425, 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) Cl 1 17.00 S 36 16.00 O 729 8.00 N 661 7.00 C 2876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.02 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 Links applied NAG-ASN " NAG A 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 780.5 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 0 sheets defined 68.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 64 through 76 Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 81 through 92 Proline residue: A 85 - end of helix Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 120 through 153 removed outlier: 4.567A pdb=" N GLY A 124 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 317 through 349 removed outlier: 3.518A pdb=" N GLY A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.511A pdb=" N TYR A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 378 through 411 Processing helix chain 'A' and resid 413 through 416 No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 420 through 439 Processing helix chain 'A' and resid 441 through 453 removed outlier: 4.367A pdb=" N ILE A 444 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 445 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.676A pdb=" N PHE A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 Processing helix chain 'A' and resid 494 through 518 removed outlier: 5.247A pdb=" N THR A 504 " --> pdb=" O TRP A 500 " (cutoff:3.500A) Proline residue: A 505 - end of helix removed outlier: 3.527A pdb=" N GLN A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 545 Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 563 through 571 249 hydrogen bonds defined for protein. 633 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: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 648 1.32 - 1.45: 1359 1.45 - 1.57: 2375 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 4440 Sorted by residual: bond pdb=" C02 TGI A 701 " pdb=" C06 TGI A 701 " ideal model delta sigma weight residual 1.599 1.413 0.186 2.00e-02 2.50e+03 8.67e+01 bond pdb=" C21 TGI A 701 " pdb=" C22 TGI A 701 " ideal model delta sigma weight residual 1.599 1.414 0.185 2.00e-02 2.50e+03 8.56e+01 bond pdb=" C20 TGI A 701 " pdb=" S24 TGI A 701 " ideal model delta sigma weight residual 1.558 1.724 -0.166 2.00e-02 2.50e+03 6.93e+01 bond pdb=" C03 TGI A 701 " pdb=" S04 TGI A 701 " ideal model delta sigma weight residual 1.558 1.723 -0.165 2.00e-02 2.50e+03 6.82e+01 bond pdb=" C23 TGI A 701 " pdb=" S24 TGI A 701 " ideal model delta sigma weight residual 1.560 1.707 -0.147 2.00e-02 2.50e+03 5.44e+01 ... (remaining 4435 not shown) Histogram of bond angle deviations from ideal: 91.51 - 100.01: 5 100.01 - 108.52: 208 108.52 - 117.03: 2721 117.03 - 125.53: 3008 125.53 - 134.04: 107 Bond angle restraints: 6049 Sorted by residual: angle pdb=" C07 TGI A 701 " pdb=" C08 TGI A 701 " pdb=" C09 TGI A 701 " ideal model delta sigma weight residual 85.79 129.01 -43.22 3.00e+00 1.11e-01 2.08e+02 angle pdb=" C03 TGI A 701 " pdb=" C07 TGI A 701 " pdb=" C20 TGI A 701 " ideal model delta sigma weight residual 92.38 120.46 -28.08 3.00e+00 1.11e-01 8.76e+01 angle pdb=" C03 TGI A 701 " pdb=" S04 TGI A 701 " pdb=" C05 TGI A 701 " ideal model delta sigma weight residual 107.57 91.51 16.06 3.00e+00 1.11e-01 2.87e+01 angle pdb=" C20 TGI A 701 " pdb=" S24 TGI A 701 " pdb=" C23 TGI A 701 " ideal model delta sigma weight residual 107.57 92.02 15.55 3.00e+00 1.11e-01 2.69e+01 angle pdb=" CA TYR A 60 " pdb=" CB TYR A 60 " pdb=" CG TYR A 60 " ideal model delta sigma weight residual 113.90 119.64 -5.74 1.80e+00 3.09e-01 1.02e+01 ... (remaining 6044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 2186 16.08 - 32.15: 279 32.15 - 48.22: 69 48.22 - 64.30: 9 64.30 - 80.37: 2 Dihedral angle restraints: 2545 sinusoidal: 1013 harmonic: 1532 Sorted by residual: dihedral pdb=" CA SER A 456 " pdb=" C SER A 456 " pdb=" N GLY A 457 " pdb=" CA GLY A 457 " ideal model delta harmonic sigma weight residual -180.00 -157.18 -22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PHE A 339 " pdb=" C PHE A 339 " pdb=" N SER A 340 " pdb=" CA SER A 340 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TRP A 116 " pdb=" C TRP A 116 " pdb=" N LYS A 117 " pdb=" CA LYS A 117 " ideal model delta harmonic sigma weight residual 180.00 158.74 21.26 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 2542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 512 0.049 - 0.099: 128 0.099 - 0.148: 27 0.148 - 0.198: 3 0.198 - 0.247: 1 Chirality restraints: 671 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C15 TGI A 701 " pdb=" C14 TGI A 701 " pdb=" C16 TGI A 701 " pdb=" C17 TGI A 701 " both_signs ideal model delta sigma weight residual False 2.73 2.55 0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA VAL A 323 " pdb=" N VAL A 323 " pdb=" C VAL A 323 " pdb=" CB VAL A 323 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 668 not shown) Planarity restraints: 736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.219 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" CG ASN A 184 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.483 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.333 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 TGI A 701 " 0.009 2.00e-02 2.50e+03 1.80e-01 4.05e+02 pdb=" C07 TGI A 701 " 0.042 2.00e-02 2.50e+03 pdb=" C08 TGI A 701 " 0.307 2.00e-02 2.50e+03 pdb=" C09 TGI A 701 " -0.210 2.00e-02 2.50e+03 pdb=" C20 TGI A 701 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " -0.099 2.00e-02 2.50e+03 1.58e-01 3.11e+02 pdb=" CG ASN A 176 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.055 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " 0.282 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " -0.173 2.00e-02 2.50e+03 ... (remaining 733 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 38 2.61 - 3.18: 4098 3.18 - 3.75: 6573 3.75 - 4.33: 9072 4.33 - 4.90: 15422 Nonbonded interactions: 35203 Sorted by model distance: nonbonded pdb=" OG1 THR A 170 " pdb=" OE2 GLU A 191 " model vdw 2.037 2.440 nonbonded pdb=" O GLY A 561 " pdb=" NH1 ARG A 566 " model vdw 2.119 2.520 nonbonded pdb=" O LEU A 279 " pdb=" OG SER A 280 " model vdw 2.258 2.440 nonbonded pdb=" O GLY A 114 " pdb=" N LYS A 117 " model vdw 2.278 2.520 nonbonded pdb=" OD1 ASN A 181 " pdb=" OG1 THR A 183 " model vdw 2.304 2.440 ... (remaining 35198 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 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.890 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.910 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 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 0.186 4440 Z= 0.563 Angle : 1.037 43.215 6049 Z= 0.463 Chirality : 0.046 0.247 671 Planarity : 0.009 0.180 733 Dihedral : 15.106 80.374 1570 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.38), residues: 530 helix: 0.55 (0.27), residues: 395 sheet: None (None), residues: 0 loop : -1.79 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 193 HIS 0.002 0.001 HIS A 347 PHE 0.016 0.002 PHE A 512 TYR 0.029 0.002 TYR A 60 ARG 0.003 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.434 Fit side-chains REVERT: A 152 TYR cc_start: 0.8218 (t80) cc_final: 0.7910 (t80) REVERT: A 314 ASN cc_start: 0.8805 (t0) cc_final: 0.8596 (t0) REVERT: A 491 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8061 (ttm170) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1638 time to fit residues: 15.2009 Evaluate side-chains 69 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 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 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4440 Z= 0.221 Angle : 0.734 17.745 6049 Z= 0.348 Chirality : 0.046 0.346 671 Planarity : 0.006 0.040 733 Dihedral : 6.564 57.523 652 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.11 % Allowed : 9.29 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.38), residues: 530 helix: 0.83 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -1.48 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.002 0.001 HIS A 347 PHE 0.018 0.001 PHE A 385 TYR 0.029 0.002 TYR A 60 ARG 0.003 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 290 THR cc_start: 0.8314 (m) cc_final: 0.7542 (p) REVERT: A 491 ARG cc_start: 0.8411 (mmm160) cc_final: 0.8015 (ttm170) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.1663 time to fit residues: 15.7381 Evaluate side-chains 69 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 47 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7517 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4440 Z= 0.194 Angle : 0.677 18.285 6049 Z= 0.318 Chirality : 0.045 0.358 671 Planarity : 0.005 0.039 733 Dihedral : 5.943 48.598 652 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.77 % Allowed : 10.62 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.38), residues: 530 helix: 1.11 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.30 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.002 0.001 HIS A 347 PHE 0.020 0.001 PHE A 474 TYR 0.024 0.001 TYR A 60 ARG 0.002 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.1141 time to fit residues: 11.8986 Evaluate side-chains 71 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.0170 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.0570 chunk 51 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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: 0.7498 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4440 Z= 0.179 Angle : 0.657 18.340 6049 Z= 0.306 Chirality : 0.043 0.358 671 Planarity : 0.005 0.039 733 Dihedral : 5.700 48.795 652 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.77 % Allowed : 13.72 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.38), residues: 530 helix: 1.17 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.21 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.001 0.001 HIS A 347 PHE 0.016 0.001 PHE A 474 TYR 0.024 0.001 TYR A 60 ARG 0.002 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.481 Fit side-chains REVERT: A 185 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.6140 (mmm) outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 0.1036 time to fit residues: 10.3978 Evaluate side-chains 69 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.7536 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4440 Z= 0.220 Angle : 0.666 18.209 6049 Z= 0.311 Chirality : 0.044 0.358 671 Planarity : 0.005 0.041 733 Dihedral : 5.718 48.118 652 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.54 % Allowed : 13.72 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.38), residues: 530 helix: 0.99 (0.27), residues: 398 sheet: None (None), residues: 0 loop : -1.25 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 230 HIS 0.001 0.001 HIS A 347 PHE 0.014 0.001 PHE A 474 TYR 0.025 0.001 TYR A 60 ARG 0.001 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.6175 (mmm) outliers start: 16 outliers final: 9 residues processed: 76 average time/residue: 0.1061 time to fit residues: 11.5445 Evaluate side-chains 73 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.7554 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4440 Z= 0.241 Angle : 0.676 18.099 6049 Z= 0.318 Chirality : 0.045 0.350 671 Planarity : 0.005 0.039 733 Dihedral : 5.727 48.739 652 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.54 % Allowed : 14.82 % Favored : 81.64 % 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: 0.62 (0.38), residues: 530 helix: 0.99 (0.27), residues: 398 sheet: None (None), residues: 0 loop : -1.26 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 230 HIS 0.001 0.000 HIS A 313 PHE 0.013 0.001 PHE A 294 TYR 0.026 0.001 TYR A 60 ARG 0.001 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.481 Fit side-chains REVERT: A 156 THR cc_start: 0.7948 (m) cc_final: 0.7720 (p) REVERT: A 185 MET cc_start: 0.6447 (OUTLIER) cc_final: 0.6007 (mmm) outliers start: 16 outliers final: 11 residues processed: 74 average time/residue: 0.1067 time to fit residues: 11.3309 Evaluate side-chains 75 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7529 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4440 Z= 0.196 Angle : 0.665 18.235 6049 Z= 0.310 Chirality : 0.044 0.351 671 Planarity : 0.005 0.042 733 Dihedral : 5.707 48.431 652 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.43 % Allowed : 16.37 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.38), residues: 530 helix: 1.01 (0.27), residues: 399 sheet: None (None), residues: 0 loop : -1.38 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 230 HIS 0.001 0.000 HIS A 347 PHE 0.012 0.001 PHE A 474 TYR 0.025 0.001 TYR A 60 ARG 0.002 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.6297 (mmp) outliers start: 11 outliers final: 9 residues processed: 70 average time/residue: 0.1041 time to fit residues: 10.4823 Evaluate side-chains 73 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7540 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 0.036 4440 Z= 0.214 Angle : 0.675 18.135 6049 Z= 0.315 Chirality : 0.044 0.353 671 Planarity : 0.005 0.041 733 Dihedral : 5.682 48.925 652 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.10 % Allowed : 15.71 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.38), residues: 530 helix: 1.00 (0.27), residues: 399 sheet: None (None), residues: 0 loop : -1.36 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.001 0.000 HIS A 313 PHE 0.011 0.001 PHE A 474 TYR 0.025 0.001 TYR A 60 ARG 0.002 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.469 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 73 average time/residue: 0.1043 time to fit residues: 11.0270 Evaluate side-chains 76 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 50 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7527 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4440 Z= 0.200 Angle : 0.670 18.174 6049 Z= 0.312 Chirality : 0.044 0.357 671 Planarity : 0.005 0.042 733 Dihedral : 5.554 48.768 652 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.88 % Allowed : 15.71 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.38), residues: 530 helix: 1.03 (0.27), residues: 399 sheet: None (None), residues: 0 loop : -1.29 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 230 HIS 0.001 0.000 HIS A 347 PHE 0.012 0.001 PHE A 474 TYR 0.025 0.001 TYR A 60 ARG 0.001 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 250 MET cc_start: 0.7599 (mmm) cc_final: 0.7339 (mmm) outliers start: 13 outliers final: 13 residues processed: 71 average time/residue: 0.1078 time to fit residues: 10.9841 Evaluate side-chains 74 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.0270 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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: 0.7533 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4440 Z= 0.207 Angle : 0.671 18.129 6049 Z= 0.313 Chirality : 0.044 0.355 671 Planarity : 0.005 0.044 733 Dihedral : 5.532 49.213 652 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.10 % Allowed : 15.71 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.38), residues: 530 helix: 1.03 (0.27), residues: 399 sheet: None (None), residues: 0 loop : -1.24 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 230 HIS 0.001 0.000 HIS A 313 PHE 0.013 0.001 PHE A 474 TYR 0.026 0.001 TYR A 60 ARG 0.001 0.000 ARG A 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.456 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 14 residues processed: 72 average time/residue: 0.1051 time to fit residues: 10.8748 Evaluate side-chains 76 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.172294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133455 restraints weight = 4489.834| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.33 r_work: 0.3445 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4440 Z= 0.195 Angle : 0.667 18.167 6049 Z= 0.310 Chirality : 0.043 0.361 671 Planarity : 0.005 0.044 733 Dihedral : 5.417 49.171 652 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.10 % Allowed : 15.71 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.38), residues: 530 helix: 1.15 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -1.28 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 230 HIS 0.001 0.000 HIS A 347 PHE 0.014 0.001 PHE A 474 TYR 0.025 0.001 TYR A 60 ARG 0.001 0.000 ARG A 318 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.04 seconds wall clock time: 23 minutes 41.14 seconds (1421.14 seconds total)