Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:02:28 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/11_2022/7n5g_24189_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/11_2022/7n5g_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_24189/11_2022/7n5g_24189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/11_2022/7n5g_24189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/11_2022/7n5g_24189_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/11_2022/7n5g_24189_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-dev-4778/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: 2.25, per 1000 atoms: 0.77 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: 1.26 Conformation dependent library (CDL) restraints added in 452.7 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: 2.13 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: 0.80 Time building geometry restraints manager: 1.36 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 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. 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: 0.800 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: 4.470 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 13.720 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 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:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: 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 *********************** 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 : 0.356 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 99 average time/residue: 1.1005 time to fit residues: 111.9228 Evaluate side-chains 85 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5084 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7891 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 2980 Z= 0.241 Angle : 0.534 5.829 4039 Z= 0.290 Chirality : 0.042 0.137 491 Planarity : 0.004 0.042 493 Dihedral : 8.337 54.184 395 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer Outliers : 4.56 % 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: 2.35 (0.43), residues: 361 helix: 2.18 (0.32), residues: 227 sheet: 0.67 (0.81), residues: 42 loop : 0.53 (0.66), residues: 92 *********************** 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 104 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.326 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 96 average time/residue: 1.1023 time to fit residues: 108.6568 Evaluate side-chains 94 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.4032 time to fit residues: 1.7216 ------------------------------------------------------------------------------- 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: 0.5980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 698 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3034 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= 0.196 Angle : 0.458 6.702 4039 Z= 0.247 Chirality : 0.039 0.127 491 Planarity : 0.003 0.017 493 Dihedral : 7.629 52.839 395 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer Outliers : 3.91 % 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: 2.55 (0.44), residues: 361 helix: 2.39 (0.33), residues: 228 sheet: 0.64 (0.77), residues: 42 loop : 0.48 (0.69), residues: 91 *********************** 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 97 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.337 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 91 average time/residue: 1.0907 time to fit residues: 101.8957 Evaluate side-chains 88 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 4 average time/residue: 0.6796 time to fit residues: 3.3003 ------------------------------------------------------------------------------- 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: 3.9990 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7925 moved from start: 0.3230 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= 0.241 Angle : 0.477 6.648 4039 Z= 0.250 Chirality : 0.040 0.124 491 Planarity : 0.003 0.022 493 Dihedral : 7.683 55.629 395 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 4.56 % 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: 2.50 (0.33), residues: 228 sheet: 0.68 (0.76), residues: 42 loop : 0.25 (0.68), residues: 91 *********************** 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 101 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.348 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 90 average time/residue: 1.1126 time to fit residues: 102.8234 Evaluate side-chains 93 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 2 residues processed: 6 average time/residue: 0.4735 time to fit residues: 3.4535 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.022 2980 Z= 0.221 Angle : 0.463 6.823 4039 Z= 0.243 Chirality : 0.040 0.146 491 Planarity : 0.003 0.020 493 Dihedral : 7.465 56.848 395 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 3.91 % 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: 2.55 (0.34), residues: 228 sheet: 0.60 (0.76), residues: 42 loop : 0.12 (0.69), residues: 91 *********************** 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: 12 poor density : 87 time to evaluate : 0.392 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 89 average time/residue: 1.1198 time to fit residues: 102.1901 Evaluate side-chains 90 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 4 average time/residue: 0.4170 time to fit residues: 2.2304 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.003 0.024 2980 Z= 0.164 Angle : 0.451 7.291 4039 Z= 0.233 Chirality : 0.039 0.143 491 Planarity : 0.003 0.016 493 Dihedral : 7.268 57.644 395 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer Outliers : 4.56 % 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: 2.68 (0.44), residues: 361 helix: 2.68 (0.33), residues: 228 sheet: 0.39 (0.75), residues: 42 loop : 0.10 (0.68), residues: 91 *********************** 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 103 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.365 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 93 average time/residue: 1.0721 time to fit residues: 102.3383 Evaluate side-chains 94 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.8086 time to fit residues: 4.6352 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.0060 chunk 7 optimal weight: 0.0010 chunk 6 optimal weight: 0.1980 overall best weight: 0.2202 ------------------------------------------------------------------------------- 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: 0.7832 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 2980 Z= 0.107 Angle : 0.409 7.789 4039 Z= 0.212 Chirality : 0.038 0.144 491 Planarity : 0.002 0.016 493 Dihedral : 7.015 56.763 395 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 3.91 % 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: 2.86 (0.33), residues: 228 sheet: 0.32 (0.76), residues: 42 loop : 0.12 (0.69), residues: 91 *********************** 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 99 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.363 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 92 average time/residue: 1.0502 time to fit residues: 99.2452 Evaluate side-chains 92 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.4166 time to fit residues: 2.2080 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7893 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 2980 Z= 0.214 Angle : 0.461 8.348 4039 Z= 0.234 Chirality : 0.039 0.132 491 Planarity : 0.003 0.015 493 Dihedral : 7.229 58.363 395 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.45), residues: 361 helix: 2.83 (0.33), residues: 228 sheet: 0.30 (0.75), residues: 42 loop : 0.19 (0.70), residues: 91 *********************** 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 99 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.394 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 1.1043 time to fit residues: 105.3229 Evaluate side-chains 93 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.4629 time to fit residues: 2.4543 ------------------------------------------------------------------------------- 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: 0.0870 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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: 0.7888 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 2980 Z= 0.159 Angle : 0.466 8.976 4039 Z= 0.234 Chirality : 0.039 0.135 491 Planarity : 0.003 0.015 493 Dihedral : 7.201 58.710 395 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer Outliers : 1.95 % 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: 2.91 (0.45), residues: 361 helix: 2.90 (0.33), residues: 228 sheet: 0.20 (0.73), residues: 42 loop : 0.23 (0.70), residues: 91 *********************** 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 93 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.347 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 89 average time/residue: 1.1358 time to fit residues: 103.6550 Evaluate side-chains 92 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.339 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.5024 time to fit residues: 2.6077 ------------------------------------------------------------------------------- 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: 0.0770 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.0370 chunk 30 optimal weight: 0.8980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 515 GLN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 2980 Z= 0.141 Angle : 0.462 9.591 4039 Z= 0.231 Chirality : 0.038 0.138 491 Planarity : 0.002 0.014 493 Dihedral : 7.182 56.563 395 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 1.95 % 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: 2.99 (0.45), residues: 361 helix: 2.99 (0.33), residues: 228 sheet: 0.15 (0.74), residues: 42 loop : 0.25 (0.71), residues: 91 ********************** 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 93 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.353 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 89 average time/residue: 1.1008 time to fit residues: 100.6031 Evaluate side-chains 92 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.5793 time to fit residues: 2.2908 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 0.0020 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.161190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.134906 restraints weight = 3965.045| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.59 r_work: 0.3845 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.3815 rms_B_bonded: 1.51 restraints_weight: 0.1250 r_work: 0.3796 rms_B_bonded: 1.69 restraints_weight: 0.0625 r_work: 0.3775 rms_B_bonded: 1.94 restraints_weight: 0.0312 r_work: 0.3750 rms_B_bonded: 2.28 restraints_weight: 0.0156 r_work: 0.3719 rms_B_bonded: 2.73 restraints_weight: 0.0078 r_work: 0.3680 rms_B_bonded: 3.32 restraints_weight: 0.0039 r_work: 0.3631 rms_B_bonded: 4.11 restraints_weight: 0.0020 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 2980 Z= 0.171 Angle : 0.497 9.857 4039 Z= 0.247 Chirality : 0.039 0.133 491 Planarity : 0.002 0.014 493 Dihedral : 7.236 54.815 395 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 1.95 % 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: 2.94 (0.45), residues: 361 helix: 2.97 (0.34), residues: 228 sheet: 0.12 (0.73), residues: 42 loop : 0.17 (0.71), residues: 91 =============================================================================== Job complete usr+sys time: 2105.75 seconds wall clock time: 37 minutes 54.20 seconds (2274.20 seconds total)