Starting phenix.real_space_refine on Thu Dec 7 16:51:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/12_2023/7n5g_24189_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/12_2023/7n5g_24189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/12_2023/7n5g_24189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/12_2023/7n5g_24189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/12_2023/7n5g_24189_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/12_2023/7n5g_24189_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1920 2.51 5 N 486 2.21 5 O 508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2926 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2926 Unusual residues: {'PLM': 1} Classifications: {'peptide': 371, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363, None: 1} Not linked: pdbres="ASN B 751 " pdbres="PLM B 801 " Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Time building chain proxies: 2.15, per 1000 atoms: 0.73 Number of scatterers: 2926 At special positions: 0 Unit cell: (70.04, 93.73, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 508 8.00 N 486 7.00 C 1920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 554.4 milliseconds 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 2 sheets defined 60.1% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 265 through 284 Processing helix chain 'B' and resid 296 through 330 removed outlier: 3.905A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 350 removed outlier: 5.033A pdb=" N ASP B 337 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 349 " --> pdb=" O HIS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 551 removed outlier: 4.134A pdb=" N ASN B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL B 529 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 589 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 4.664A pdb=" N THR B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 677 Processing helix chain 'B' and resid 715 through 735 Processing sheet with id= A, first strand: chain 'B' and resid 639 through 641 removed outlier: 6.842A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.749A pdb=" N ALA B 703 " --> pdb=" O VAL B 691 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL B 691 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE B 705 " --> pdb=" O MET B 689 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N MET B 689 " --> pdb=" O PHE B 705 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 534 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: 0.74 Time building geometry restraints manager: 1.33 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: 675 1.32 - 1.44: 718 1.44 - 1.57: 1550 1.57 - 1.69: 16 1.69 - 1.81: 21 Bond restraints: 2980 Sorted by residual: bond pdb=" CD2 TRP B 507 " pdb=" CE3 TRP B 507 " ideal model delta sigma weight residual 1.398 1.503 -0.105 1.60e-02 3.91e+03 4.27e+01 bond pdb=" CZ2 TRP B 507 " pdb=" CH2 TRP B 507 " ideal model delta sigma weight residual 1.368 1.480 -0.112 1.90e-02 2.77e+03 3.46e+01 bond pdb=" CB ILE B 285 " pdb=" CG1 ILE B 285 " ideal model delta sigma weight residual 1.530 1.635 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" CB TYR B 629 " pdb=" CG TYR B 629 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.65e+01 bond pdb=" CB HIS B 345 " pdb=" CG HIS B 345 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.46e+01 ... (remaining 2975 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.94: 53 105.94 - 113.05: 1626 113.05 - 120.16: 1256 120.16 - 127.27: 1072 127.27 - 134.38: 32 Bond angle restraints: 4039 Sorted by residual: angle pdb=" C HIS B 592 " pdb=" N PRO B 593 " pdb=" CA PRO B 593 " ideal model delta sigma weight residual 119.56 126.54 -6.98 1.01e+00 9.80e-01 4.78e+01 angle pdb=" C SER B 645 " pdb=" N PRO B 646 " pdb=" CA PRO B 646 " ideal model delta sigma weight residual 120.52 126.91 -6.39 9.90e-01 1.02e+00 4.17e+01 angle pdb=" C LEU B 743 " pdb=" N PRO B 744 " pdb=" CA PRO B 744 " ideal model delta sigma weight residual 119.85 126.24 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C GLN B 291 " pdb=" N PRO B 292 " pdb=" CA PRO B 292 " ideal model delta sigma weight residual 119.28 125.41 -6.13 1.10e+00 8.26e-01 3.11e+01 angle pdb=" N SER B 267 " pdb=" CA SER B 267 " pdb=" C SER B 267 " ideal model delta sigma weight residual 112.23 105.58 6.65 1.26e+00 6.30e-01 2.79e+01 ... (remaining 4034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 1685 14.33 - 28.65: 62 28.65 - 42.97: 7 42.97 - 57.30: 11 57.30 - 71.62: 6 Dihedral angle restraints: 1771 sinusoidal: 680 harmonic: 1091 Sorted by residual: dihedral pdb=" CA ASP B 657 " pdb=" CB ASP B 657 " pdb=" CG ASP B 657 " pdb=" OD1 ASP B 657 " ideal model delta sinusoidal sigma weight residual -30.00 -84.87 54.87 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP B 595 " pdb=" CB ASP B 595 " pdb=" CG ASP B 595 " pdb=" OD1 ASP B 595 " ideal model delta sinusoidal sigma weight residual -30.00 -74.43 44.43 1 2.00e+01 2.50e-03 6.86e+00 dihedral pdb=" N ASP B 650 " pdb=" C ASP B 650 " pdb=" CA ASP B 650 " pdb=" CB ASP B 650 " ideal model delta harmonic sigma weight residual 122.80 116.39 6.41 0 2.50e+00 1.60e-01 6.57e+00 ... (remaining 1768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 371 0.097 - 0.193: 99 0.193 - 0.290: 16 0.290 - 0.387: 3 0.387 - 0.483: 2 Chirality restraints: 491 Sorted by residual: chirality pdb=" CG LEU B 264 " pdb=" CB LEU B 264 " pdb=" CD1 LEU B 264 " pdb=" CD2 LEU B 264 " both_signs ideal model delta sigma weight residual False -2.59 -3.07 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CB ILE B 285 " pdb=" CA ILE B 285 " pdb=" CG1 ILE B 285 " pdb=" CG2 ILE B 285 " both_signs ideal model delta sigma weight residual False 2.64 3.05 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA TRP B 304 " pdb=" N TRP B 304 " pdb=" C TRP B 304 " pdb=" CB TRP B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 488 not shown) Planarity restraints: 493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 697 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C VAL B 697 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL B 697 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN B 698 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 675 " 0.035 2.00e-02 2.50e+03 1.98e-02 7.85e+00 pdb=" CG TYR B 675 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 675 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 675 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 675 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 675 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 675 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 675 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 741 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C ASN B 741 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN B 741 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 742 " -0.014 2.00e-02 2.50e+03 ... (remaining 490 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1129 2.89 - 3.39: 3007 3.39 - 3.89: 4769 3.89 - 4.40: 5456 4.40 - 4.90: 8449 Nonbonded interactions: 22810 Sorted by model distance: nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 2.520 nonbonded pdb=" N VAL B 697 " pdb=" N ASN B 698 " model vdw 2.467 2.560 nonbonded pdb=" N ASN B 711 " pdb=" O ASN B 711 " model vdw 2.498 2.496 nonbonded pdb=" N PRO B 646 " pdb=" O PRO B 646 " model vdw 2.533 2.496 nonbonded pdb=" N ASN B 613 " pdb=" O ASN B 613 " model vdw 2.553 2.496 ... (remaining 22805 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: 0.960 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: 4.400 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.280 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.022 0.132 2980 Z= 1.475 Angle : 1.511 8.243 4039 Z= 1.034 Chirality : 0.093 0.483 491 Planarity : 0.008 0.031 493 Dihedral : 10.569 71.622 1051 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.41), residues: 361 helix: 1.41 (0.30), residues: 223 sheet: 0.94 (0.88), residues: 42 loop : 1.21 (0.65), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.008 TRP B 683 HIS 0.005 0.002 HIS B 346 PHE 0.019 0.005 PHE B 682 TYR 0.035 0.008 TYR B 675 ARG 0.005 0.001 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.333 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 99 average time/residue: 1.1235 time to fit residues: 114.0923 Evaluate side-chains 85 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.339 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 605 ASN B 648 GLN B 688 ASN B 698 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 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 : 0.004 0.025 2980 Z= 0.236 Angle : 0.531 5.848 4039 Z= 0.289 Chirality : 0.042 0.137 491 Planarity : 0.004 0.039 493 Dihedral : 8.339 54.195 395 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.56 % Allowed : 10.42 % Favored : 85.02 % 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: 2.34 (0.43), residues: 361 helix: 2.17 (0.32), residues: 227 sheet: 0.67 (0.81), residues: 42 loop : 0.53 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 281 HIS 0.004 0.001 HIS B 346 PHE 0.014 0.002 PHE B 594 TYR 0.006 0.002 TYR B 740 ARG 0.004 0.001 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.348 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 95 average time/residue: 1.2287 time to fit residues: 119.5541 Evaluate side-chains 94 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.335 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.4193 time to fit residues: 1.8140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2980 Z= 0.161 Angle : 0.446 6.794 4039 Z= 0.240 Chirality : 0.039 0.127 491 Planarity : 0.003 0.017 493 Dihedral : 7.849 53.057 395 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.91 % Allowed : 12.70 % Favored : 83.39 % 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: 2.59 (0.44), residues: 361 helix: 2.43 (0.33), residues: 228 sheet: 0.60 (0.77), residues: 42 loop : 0.49 (0.69), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 281 HIS 0.003 0.001 HIS B 346 PHE 0.009 0.001 PHE B 715 TYR 0.008 0.001 TYR B 740 ARG 0.003 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.362 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 91 average time/residue: 1.1886 time to fit residues: 110.8619 Evaluate side-chains 87 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.322 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.3621 time to fit residues: 3.2327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 33 optimal weight: 0.0060 chunk 35 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2980 Z= 0.115 Angle : 0.416 7.520 4039 Z= 0.218 Chirality : 0.038 0.127 491 Planarity : 0.003 0.016 493 Dihedral : 7.568 53.070 395 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.23 % Allowed : 13.03 % 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: 2.87 (0.44), residues: 361 helix: 2.74 (0.33), residues: 228 sheet: 0.55 (0.77), residues: 42 loop : 0.43 (0.70), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 316 HIS 0.002 0.001 HIS B 346 PHE 0.007 0.001 PHE B 654 TYR 0.006 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.360 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 92 average time/residue: 1.1783 time to fit residues: 111.1275 Evaluate side-chains 90 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.8884 time to fit residues: 3.2208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2980 Z= 0.201 Angle : 0.458 6.573 4039 Z= 0.238 Chirality : 0.039 0.124 491 Planarity : 0.003 0.017 493 Dihedral : 7.617 58.598 395 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.26 % Allowed : 15.64 % Favored : 81.11 % 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: 2.79 (0.44), residues: 361 helix: 2.72 (0.33), residues: 228 sheet: 0.53 (0.75), residues: 42 loop : 0.26 (0.67), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.012 0.001 PHE B 271 TYR 0.008 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.352 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 1.1750 time to fit residues: 110.6955 Evaluate side-chains 93 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.3897 time to fit residues: 2.5055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2980 Z= 0.144 Angle : 0.435 7.231 4039 Z= 0.224 Chirality : 0.039 0.152 491 Planarity : 0.003 0.014 493 Dihedral : 7.388 56.769 395 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.91 % Allowed : 15.64 % Favored : 80.46 % 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: 2.88 (0.45), residues: 361 helix: 2.82 (0.33), residues: 228 sheet: 0.44 (0.78), residues: 42 loop : 0.28 (0.69), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 PHE 0.009 0.001 PHE B 572 TYR 0.006 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.369 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 91 average time/residue: 1.2262 time to fit residues: 114.2990 Evaluate side-chains 91 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 4 average time/residue: 0.7348 time to fit residues: 3.5160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.0050 chunk 7 optimal weight: 0.0170 chunk 6 optimal weight: 0.5980 overall best weight: 0.2570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2980 Z= 0.111 Angle : 0.429 8.135 4039 Z= 0.218 Chirality : 0.038 0.150 491 Planarity : 0.002 0.015 493 Dihedral : 7.230 56.433 395 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.63 % Allowed : 18.24 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.45), residues: 361 helix: 2.87 (0.33), residues: 228 sheet: 0.33 (0.76), residues: 42 loop : 0.29 (0.70), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 548 HIS 0.002 0.000 HIS B 708 PHE 0.009 0.001 PHE B 572 TYR 0.005 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.340 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 1.1766 time to fit residues: 107.3712 Evaluate side-chains 90 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.7762 time to fit residues: 2.0746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2980 Z= 0.210 Angle : 0.495 8.080 4039 Z= 0.250 Chirality : 0.040 0.140 491 Planarity : 0.003 0.016 493 Dihedral : 7.361 59.067 395 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.26 % Allowed : 16.29 % Favored : 80.46 % 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: 2.84 (0.45), residues: 361 helix: 2.83 (0.34), residues: 228 sheet: 0.24 (0.74), residues: 42 loop : 0.20 (0.70), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.012 0.001 PHE B 271 TYR 0.007 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.398 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 1.1156 time to fit residues: 104.2096 Evaluate side-chains 91 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.4428 time to fit residues: 2.3433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.2980 chunk 10 optimal weight: 0.0060 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2980 Z= 0.181 Angle : 0.504 10.532 4039 Z= 0.248 Chirality : 0.040 0.148 491 Planarity : 0.003 0.014 493 Dihedral : 7.378 59.436 395 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.30 % Allowed : 18.89 % Favored : 79.80 % 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: 2.85 (0.45), residues: 361 helix: 2.87 (0.34), residues: 228 sheet: 0.17 (0.74), residues: 42 loop : 0.18 (0.70), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 PHE 0.010 0.001 PHE B 654 TYR 0.006 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.339 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 87 average time/residue: 1.1948 time to fit residues: 106.5144 Evaluate side-chains 89 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.8873 time to fit residues: 2.3097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2980 Z= 0.168 Angle : 0.497 9.727 4039 Z= 0.245 Chirality : 0.039 0.143 491 Planarity : 0.003 0.014 493 Dihedral : 7.405 59.818 395 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.30 % Allowed : 18.89 % Favored : 79.80 % 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: 2.86 (0.45), residues: 361 helix: 2.94 (0.34), residues: 225 sheet: 0.10 (0.73), residues: 42 loop : 0.13 (0.68), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 PHE 0.010 0.001 PHE B 572 TYR 0.006 0.001 TYR B 740 ARG 0.001 0.000 ARG B 722 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.341 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 88 average time/residue: 1.2242 time to fit residues: 110.3348 Evaluate side-chains 88 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.6580 time to fit residues: 1.8856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.0170 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 0.0010 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 515 GLN B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.161999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.137845 restraints weight = 4000.261| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.75 r_work: 0.3758 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2980 Z= 0.158 Angle : 0.506 11.913 4039 Z= 0.246 Chirality : 0.039 0.144 491 Planarity : 0.002 0.015 493 Dihedral : 7.446 59.989 395 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.28 % Allowed : 17.59 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.45), residues: 361 helix: 3.00 (0.34), residues: 225 sheet: 0.11 (0.73), residues: 42 loop : 0.15 (0.69), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 PHE 0.010 0.001 PHE B 572 TYR 0.006 0.001 TYR B 740 ARG 0.001 0.000 ARG B 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2404.15 seconds wall clock time: 43 minutes 10.51 seconds (2590.51 seconds total)