Starting phenix.real_space_refine (version: dev) on Sun Dec 11 14:08:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/12_2022/7wxg_32878_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/12_2022/7wxg_32878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/12_2022/7wxg_32878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/12_2022/7wxg_32878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/12_2022/7wxg_32878_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/12_2022/7wxg_32878_updated.pdb" } resolution = 4.2 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= 0.000 sd= 0.005 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 "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A ASP 548": "OD1" <-> "OD2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ASP 668": "OD1" <-> "OD2" Residue "A ASP 683": "OD1" <-> "OD2" Residue "A ASP 690": "OD1" <-> "OD2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 3295 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3295 Unusual residues: {'NAP': 1} Inner-chain residues flagged as termini: ['pdbres="ASP A 776 "'] Classifications: {'peptide': 430, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414, None: 1} Not linked: pdbres="ASP A 776 " pdbres="NAP A 801 " Time building chain proxies: 2.54, per 1000 atoms: 0.77 Number of scatterers: 3295 At special positions: 0 Unit cell: (80.56, 93.28, 60.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 3 15.00 O 636 8.00 N 593 7.00 C 2048 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: 1.45 Conformation dependent library (CDL) restraints added in 517.4 milliseconds 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 4 sheets defined 43.0% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 367 through 402 removed outlier: 3.676A pdb=" N SER A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LYS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 416 through 431 Processing helix chain 'A' and resid 472 through 483 Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.468A pdb=" N THR A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 580 through 591 Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 690 through 699 Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing sheet with id= A, first strand: chain 'A' and resid 744 through 752 removed outlier: 3.650A pdb=" N ILE A 749 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 751 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 442 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR A 456 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 440 " --> pdb=" O THR A 456 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 486 through 488 removed outlier: 6.545A pdb=" N LEU A 540 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE A 465 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE A 542 " --> pdb=" O ILE A 465 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 604 through 607 Processing sheet with id= D, first strand: chain 'A' and resid 683 through 685 132 hydrogen bonds defined for protein. 396 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: 0.85 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 571 1.31 - 1.43: 791 1.43 - 1.56: 1955 1.56 - 1.68: 8 1.68 - 1.81: 24 Bond restraints: 3349 Sorted by residual: bond pdb=" C1D NAP A 801 " pdb=" C2D NAP A 801 " ideal model delta sigma weight residual 1.533 1.271 0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C3D NAP A 801 " pdb=" C4D NAP A 801 " ideal model delta sigma weight residual 1.518 1.261 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C3B NAP A 801 " pdb=" C4B NAP A 801 " ideal model delta sigma weight residual 1.543 1.294 0.249 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C4B NAP A 801 " pdb=" O4B NAP A 801 " ideal model delta sigma weight residual 1.426 1.623 -0.197 2.00e-02 2.50e+03 9.67e+01 bond pdb=" C1D NAP A 801 " pdb=" O4D NAP A 801 " ideal model delta sigma weight residual 1.375 1.550 -0.175 2.00e-02 2.50e+03 7.65e+01 ... (remaining 3344 not shown) Histogram of bond angle deviations from ideal: 99.46 - 108.69: 214 108.69 - 117.92: 2411 117.92 - 127.15: 1886 127.15 - 136.39: 31 136.39 - 145.62: 2 Bond angle restraints: 4544 Sorted by residual: angle pdb=" N1A NAP A 801 " pdb=" C6A NAP A 801 " pdb=" N6A NAP A 801 " ideal model delta sigma weight residual 119.30 99.46 19.84 3.00e+00 1.11e-01 4.37e+01 angle pdb=" C1B NAP A 801 " pdb=" N9A NAP A 801 " pdb=" C4A NAP A 801 " ideal model delta sigma weight residual 124.31 107.08 17.23 3.00e+00 1.11e-01 3.30e+01 angle pdb=" C5A NAP A 801 " pdb=" C6A NAP A 801 " pdb=" N6A NAP A 801 " ideal model delta sigma weight residual 122.73 139.91 -17.18 3.00e+00 1.11e-01 3.28e+01 angle pdb=" C1B NAP A 801 " pdb=" N9A NAP A 801 " pdb=" C8A NAP A 801 " ideal model delta sigma weight residual 129.84 145.62 -15.78 3.00e+00 1.11e-01 2.77e+01 angle pdb=" O1N NAP A 801 " pdb=" PN NAP A 801 " pdb=" O2N NAP A 801 " ideal model delta sigma weight residual 122.51 109.58 12.93 3.00e+00 1.11e-01 1.86e+01 ... (remaining 4539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.77: 1751 14.77 - 29.54: 211 29.54 - 44.30: 67 44.30 - 59.07: 6 59.07 - 73.84: 4 Dihedral angle restraints: 2039 sinusoidal: 807 harmonic: 1232 Sorted by residual: dihedral pdb=" CA PHE A 642 " pdb=" C PHE A 642 " pdb=" N GLY A 643 " pdb=" CA GLY A 643 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA CYS A 598 " pdb=" C CYS A 598 " pdb=" N ASN A 599 " pdb=" CA ASN A 599 " ideal model delta harmonic sigma weight residual -180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ALA A 714 " pdb=" C ALA A 714 " pdb=" N ASP A 715 " pdb=" CA ASP A 715 " ideal model delta harmonic sigma weight residual 180.00 164.01 15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 2036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 466 0.072 - 0.144: 58 0.144 - 0.215: 5 0.215 - 0.287: 1 0.287 - 0.359: 1 Chirality restraints: 531 Sorted by residual: chirality pdb=" C3D NAP A 801 " pdb=" C2D NAP A 801 " pdb=" C4D NAP A 801 " pdb=" O3D NAP A 801 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C2B NAP A 801 " pdb=" C1B NAP A 801 " pdb=" C3B NAP A 801 " pdb=" O2B NAP A 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.50 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C2D NAP A 801 " pdb=" C1D NAP A 801 " pdb=" C3D NAP A 801 " pdb=" O2D NAP A 801 " both_signs ideal model delta sigma weight residual False -2.55 -2.37 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 528 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 560 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO A 561 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 594 " 0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO A 595 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 469 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 470 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " 0.018 5.00e-02 4.00e+02 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 282 2.73 - 3.27: 3698 3.27 - 3.81: 5285 3.81 - 4.36: 6013 4.36 - 4.90: 10085 Nonbonded interactions: 25363 Sorted by model distance: nonbonded pdb=" O SER A 410 " pdb=" OG SER A 413 " model vdw 2.184 2.440 nonbonded pdb=" O CYS A 570 " pdb=" ND1 HIS A 571 " model vdw 2.185 2.520 nonbonded pdb=" O ASP A 530 " pdb=" OG SER A 533 " model vdw 2.254 2.440 nonbonded pdb=" O ALA A 399 " pdb=" OG SER A 402 " model vdw 2.257 2.440 nonbonded pdb=" NH1 ARG A 525 " pdb=" O4B NAP A 801 " model vdw 2.272 2.520 ... (remaining 25358 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 15 5.16 5 C 2048 2.51 5 N 593 2.21 5 O 636 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 5.730 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 14.290 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 0.012 0.262 3349 Z= 0.741 Angle : 1.073 19.838 4544 Z= 0.492 Chirality : 0.050 0.359 531 Planarity : 0.004 0.033 588 Dihedral : 14.216 73.837 1241 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer Outliers : 0.29 % 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: -5.16 (0.29), residues: 428 helix: -2.48 (0.29), residues: 186 sheet: -4.14 (0.44), residues: 61 loop : -4.14 (0.33), residues: 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.413 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1936 time to fit residues: 19.4163 Evaluate side-chains 60 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 434 HIS A 497 HIS A 607 HIS A 673 HIS A 681 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3349 Z= 0.152 Angle : 0.609 5.838 4544 Z= 0.303 Chirality : 0.044 0.153 531 Planarity : 0.004 0.043 588 Dihedral : 6.126 37.975 480 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.36), residues: 428 helix: -0.73 (0.35), residues: 187 sheet: -3.32 (0.49), residues: 60 loop : -2.91 (0.42), residues: 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.403 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.1620 time to fit residues: 18.0438 Evaluate side-chains 63 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 556 GLN A 652 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3349 Z= 0.148 Angle : 0.571 6.142 4544 Z= 0.283 Chirality : 0.043 0.171 531 Planarity : 0.004 0.048 588 Dihedral : 5.895 37.565 480 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 0.58 % 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: -2.07 (0.39), residues: 428 helix: 0.15 (0.37), residues: 187 sheet: -2.78 (0.53), residues: 61 loop : -2.50 (0.44), residues: 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 90 average time/residue: 0.1420 time to fit residues: 15.9410 Evaluate side-chains 58 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 695 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 3349 Z= 0.155 Angle : 0.577 7.360 4544 Z= 0.283 Chirality : 0.043 0.174 531 Planarity : 0.004 0.046 588 Dihedral : 5.867 39.120 480 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 0.29 % 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: -1.53 (0.40), residues: 428 helix: 0.59 (0.37), residues: 186 sheet: -2.51 (0.54), residues: 63 loop : -2.17 (0.46), residues: 179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.425 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.1415 time to fit residues: 15.6999 Evaluate side-chains 59 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.018 3349 Z= 0.170 Angle : 0.601 6.999 4544 Z= 0.295 Chirality : 0.042 0.169 531 Planarity : 0.004 0.045 588 Dihedral : 5.936 39.047 480 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % 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: -1.23 (0.41), residues: 428 helix: 0.89 (0.38), residues: 186 sheet: -2.37 (0.55), residues: 61 loop : -2.07 (0.46), residues: 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.421 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1566 time to fit residues: 17.2582 Evaluate side-chains 58 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.0020 chunk 3 optimal weight: 0.0370 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.4866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN A 770 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 3349 Z= 0.136 Angle : 0.580 7.054 4544 Z= 0.283 Chirality : 0.041 0.158 531 Planarity : 0.004 0.043 588 Dihedral : 5.767 38.764 480 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.41), residues: 428 helix: 1.01 (0.39), residues: 192 sheet: -2.01 (0.57), residues: 63 loop : -1.79 (0.48), residues: 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.425 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1467 time to fit residues: 16.4417 Evaluate side-chains 60 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 770 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 3349 Z= 0.234 Angle : 0.613 7.781 4544 Z= 0.307 Chirality : 0.043 0.177 531 Planarity : 0.004 0.041 588 Dihedral : 6.043 41.615 480 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.41), residues: 428 helix: 1.15 (0.39), residues: 186 sheet: -2.09 (0.57), residues: 63 loop : -1.95 (0.46), residues: 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.422 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1569 time to fit residues: 16.2376 Evaluate side-chains 59 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 3349 Z= 0.155 Angle : 0.595 8.147 4544 Z= 0.291 Chirality : 0.042 0.146 531 Planarity : 0.004 0.042 588 Dihedral : 5.905 42.562 480 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.42), residues: 428 helix: 1.39 (0.40), residues: 186 sheet: -1.80 (0.59), residues: 62 loop : -1.88 (0.46), residues: 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.415 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1395 time to fit residues: 14.4414 Evaluate side-chains 59 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3349 Z= 0.183 Angle : 0.608 8.629 4544 Z= 0.300 Chirality : 0.043 0.157 531 Planarity : 0.004 0.040 588 Dihedral : 5.967 43.997 480 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.42), residues: 428 helix: 1.26 (0.39), residues: 191 sheet: -1.80 (0.60), residues: 63 loop : -1.80 (0.47), residues: 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1575 time to fit residues: 16.9482 Evaluate side-chains 64 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3349 Z= 0.195 Angle : 0.624 8.849 4544 Z= 0.308 Chirality : 0.043 0.147 531 Planarity : 0.004 0.040 588 Dihedral : 6.049 45.753 480 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.41), residues: 428 helix: 1.20 (0.39), residues: 191 sheet: -1.88 (0.59), residues: 63 loop : -1.80 (0.47), residues: 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1555 time to fit residues: 16.5816 Evaluate side-chains 61 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.405 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103505 restraints weight = 6537.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106784 restraints weight = 4182.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109149 restraints weight = 3036.057| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 3349 Z= 0.155 Angle : 0.599 8.747 4544 Z= 0.293 Chirality : 0.042 0.134 531 Planarity : 0.004 0.041 588 Dihedral : 5.925 47.205 480 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.42), residues: 428 helix: 1.31 (0.39), residues: 191 sheet: -1.77 (0.60), residues: 63 loop : -1.76 (0.47), residues: 174 =============================================================================== Job complete usr+sys time: 1192.36 seconds wall clock time: 22 minutes 12.52 seconds (1332.52 seconds total)