Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 16:16:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/08_2023/7y7z_33675_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/08_2023/7y7z_33675.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/08_2023/7y7z_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_33675/08_2023/7y7z_33675_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/08_2023/7y7z_33675_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/08_2023/7y7z_33675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/08_2023/7y7z_33675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/08_2023/7y7z_33675_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7z_33675/08_2023/7y7z_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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 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: 1.77 Conformation dependent library (CDL) restraints added in 617.5 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: 0.72 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: 1.25 Time building geometry restraints manager: 1.87 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: 2127 16.08 - 32.15: 273 32.15 - 48.22: 69 48.22 - 64.30: 8 64.30 - 80.37: 2 Dihedral angle restraints: 2479 sinusoidal: 947 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 2476 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: 0.420 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: 2.070 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.310 Find NCS groups from input model: 0.110 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- 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 : 15.224 80.374 1504 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 % 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 *********************** 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 : 0.487 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1683 time to fit residues: 15.6227 Evaluate side-chains 66 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.456 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6284 ------------------------------------------------------------------------------- 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: 3.9990 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 A 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4440 Z= 0.223 Angle : 0.739 16.472 6049 Z= 0.350 Chirality : 0.046 0.344 671 Planarity : 0.006 0.040 733 Dihedral : 6.062 56.772 586 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.38), residues: 530 helix: 0.81 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -1.49 (0.55), residues: 137 *********************** 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 73 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.424 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.1550 time to fit residues: 14.4443 Evaluate side-chains 66 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.464 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.0454 time to fit residues: 0.9739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 47 optimal weight: 0.0010 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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: 0.7571 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 4440 Z= 0.261 Angle : 0.708 17.826 6049 Z= 0.337 Chirality : 0.046 0.356 671 Planarity : 0.005 0.039 733 Dihedral : 5.815 50.091 586 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 0.88 % 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: 0.47 (0.38), residues: 530 helix: 1.00 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.44 (0.52), residues: 148 *********************** 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 72 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.489 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.1541 time to fit residues: 14.4288 Evaluate side-chains 65 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.459 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0525 time to fit residues: 0.8966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.0050 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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: 0.7541 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4440 Z= 0.209 Angle : 0.680 18.209 6049 Z= 0.321 Chirality : 0.044 0.353 671 Planarity : 0.005 0.039 733 Dihedral : 5.669 49.556 586 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 1.55 % 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: 0.58 (0.38), residues: 530 helix: 1.04 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.29 (0.53), residues: 147 *********************** 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 78 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 75 average time/residue: 0.1467 time to fit residues: 14.5210 Evaluate side-chains 68 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.469 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0437 time to fit residues: 0.7654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7555 moved from start: 0.1947 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= 0.227 Angle : 0.677 18.158 6049 Z= 0.319 Chirality : 0.044 0.348 671 Planarity : 0.005 0.041 733 Dihedral : 5.577 48.754 586 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.38), residues: 530 helix: 1.04 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -1.24 (0.54), residues: 139 *********************** 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 72 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.469 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.1401 time to fit residues: 13.2813 Evaluate side-chains 67 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.429 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0465 time to fit residues: 0.8510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 0.0770 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4440 Z= 0.185 Angle : 0.666 18.272 6049 Z= 0.311 Chirality : 0.043 0.353 671 Planarity : 0.005 0.039 733 Dihedral : 5.498 47.897 586 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.38), residues: 530 helix: 0.98 (0.27), residues: 398 sheet: None (None), residues: 0 loop : -1.22 (0.56), residues: 132 *********************** 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 67 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 66 average time/residue: 0.1082 time to fit residues: 10.3496 Evaluate side-chains 61 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.447 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0429 time to fit residues: 0.7634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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: 0.7546 moved from start: 0.2221 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= 0.217 Angle : 0.670 18.129 6049 Z= 0.313 Chirality : 0.043 0.349 671 Planarity : 0.005 0.041 733 Dihedral : 5.475 48.397 586 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.38), residues: 530 helix: 1.01 (0.27), residues: 397 sheet: None (None), residues: 0 loop : -1.29 (0.54), residues: 133 *********************** 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 69 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.453 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.1099 time to fit residues: 10.8528 Evaluate side-chains 67 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.456 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0674 time to fit residues: 1.3376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7537 moved from start: 0.2274 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= 0.210 Angle : 0.683 18.157 6049 Z= 0.321 Chirality : 0.044 0.350 671 Planarity : 0.005 0.041 733 Dihedral : 5.477 48.492 586 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 0.88 % 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: 0.58 (0.38), residues: 530 helix: 0.97 (0.27), residues: 399 sheet: None (None), residues: 0 loop : -1.31 (0.54), residues: 131 *********************** 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 67 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 0.1120 time to fit residues: 10.5475 Evaluate side-chains 65 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.401 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0472 time to fit residues: 0.9322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7535 moved from start: 0.2363 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= 0.206 Angle : 0.682 18.151 6049 Z= 0.321 Chirality : 0.043 0.345 671 Planarity : 0.005 0.043 733 Dihedral : 5.440 48.503 586 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.38), residues: 530 helix: 0.98 (0.27), residues: 399 sheet: None (None), residues: 0 loop : -1.27 (0.55), residues: 131 *********************** 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 63 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.1124 time to fit residues: 10.1380 Evaluate side-chains 62 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.454 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0459 time to fit residues: 0.6966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 0.0170 chunk 4 optimal weight: 0.1980 chunk 32 optimal weight: 0.0070 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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: 0.7492 moved from start: 0.2531 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= 0.162 Angle : 0.671 18.324 6049 Z= 0.312 Chirality : 0.043 0.343 671 Planarity : 0.005 0.043 733 Dihedral : 5.307 47.661 586 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.44 % 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: 0.73 (0.38), residues: 530 helix: 1.05 (0.27), residues: 400 sheet: None (None), residues: 0 loop : -1.13 (0.56), residues: 130 ********************** 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 66 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.1131 time to fit residues: 10.5568 Evaluate side-chains 64 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.602 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0596 time to fit residues: 0.7309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.177669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136935 restraints weight = 4681.745| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.00 r_work: 0.3154 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2471 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= 0.218 Angle : 0.693 18.073 6049 Z= 0.323 Chirality : 0.043 0.346 671 Planarity : 0.005 0.043 733 Dihedral : 5.369 48.720 586 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.38), residues: 530 helix: 1.04 (0.27), residues: 399 sheet: None (None), residues: 0 loop : -1.19 (0.56), residues: 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1268.56 seconds wall clock time: 23 minutes 32.75 seconds (1412.75 seconds total)