Starting phenix.real_space_refine on Fri Dec 8 02:29:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8x_24248/12_2023/7n8x_24248.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8x_24248/12_2023/7n8x_24248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8x_24248/12_2023/7n8x_24248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8x_24248/12_2023/7n8x_24248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8x_24248/12_2023/7n8x_24248.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8x_24248/12_2023/7n8x_24248.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.023 sd= 0.773 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4202 2.51 5 N 1073 2.21 5 O 1319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 438": "OE1" <-> "OE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 765": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A ASP 1862": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6617 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1093 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 13, 'TRANS': 126} Chain: "A" Number of atoms: 5524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5524 Classifications: {'peptide': 691} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 669} Chain breaks: 1 Time building chain proxies: 4.27, per 1000 atoms: 0.65 Number of scatterers: 6617 At special positions: 0 Unit cell: (109.61, 84.75, 91.53, 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 23 16.00 O 1319 8.00 N 1073 7.00 C 4202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 124 " distance=2.03 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: 2.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1580 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 29.0% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'A' and resid 398 through 415 Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.708A pdb=" N GLU A 420 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 438 removed outlier: 3.657A pdb=" N GLU A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 removed outlier: 4.326A pdb=" N GLU A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.616A pdb=" N LEU A 454 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 456 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 removed outlier: 3.513A pdb=" N ASN A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.334A pdb=" N ALA A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 523 through 539 removed outlier: 4.483A pdb=" N ALA A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 588 through 601 removed outlier: 4.026A pdb=" N THR A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 682 Processing helix chain 'A' and resid 710 through 727 removed outlier: 4.533A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 775 removed outlier: 3.741A pdb=" N ILE A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 809 Processing helix chain 'A' and resid 814 through 836 Processing helix chain 'A' and resid 1773 through 1778 removed outlier: 3.690A pdb=" N ASN A1778 " --> pdb=" O LYS A1774 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1796 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.870A pdb=" N VAL B 30 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 135 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 110 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 65 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.870A pdb=" N VAL B 30 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 135 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 110 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 65 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 37 Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 629 removed outlier: 4.517A pdb=" N TYR A 621 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N SER A 605 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 649 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 646 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ASN A 694 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 648 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU A 696 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE A 650 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 744 through 746 Processing sheet with id=AA6, first strand: chain 'A' and resid 1654 through 1657 removed outlier: 5.879A pdb=" N MET A1655 " --> pdb=" O VAL A1692 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A1691 " --> pdb=" O ILE A1718 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A1765 " --> pdb=" O LEU A1751 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1701 through 1704 removed outlier: 6.043A pdb=" N ILE A1702 " --> pdb=" O ASN A1732 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A1731 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1844 through 1845 removed outlier: 4.631A pdb=" N TYR A1844 " --> pdb=" O ILE A1853 " (cutoff:3.500A) 190 hydrogen bonds defined for protein. 504 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: 2.08 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2171 1.34 - 1.46: 927 1.46 - 1.57: 3604 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 6741 Sorted by residual: bond pdb=" C VAL B 43 " pdb=" O VAL B 43 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.19e-02 7.06e+03 1.84e+00 bond pdb=" N ASP A 614 " pdb=" CA ASP A 614 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.70e+00 bond pdb=" CB PRO A 644 " pdb=" CG PRO A 644 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.45e+00 bond pdb=" C PRO A1847 " pdb=" N PRO A1848 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.33e+00 bond pdb=" CG1 ILE A 578 " pdb=" CD1 ILE A 578 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.09e+00 ... (remaining 6736 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.89: 131 105.89 - 112.91: 3547 112.91 - 119.94: 2349 119.94 - 126.96: 3061 126.96 - 133.99: 50 Bond angle restraints: 9138 Sorted by residual: angle pdb=" C LEU A 519 " pdb=" CA LEU A 519 " pdb=" CB LEU A 519 " ideal model delta sigma weight residual 116.63 111.22 5.41 1.16e+00 7.43e-01 2.18e+01 angle pdb=" CA LEU B 72 " pdb=" CB LEU B 72 " pdb=" CG LEU B 72 " ideal model delta sigma weight residual 116.30 129.98 -13.68 3.50e+00 8.16e-02 1.53e+01 angle pdb=" CG1 ILE A 640 " pdb=" CB ILE A 640 " pdb=" CG2 ILE A 640 " ideal model delta sigma weight residual 110.70 99.57 11.13 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA PRO A 644 " pdb=" N PRO A 644 " pdb=" CD PRO A 644 " ideal model delta sigma weight residual 112.00 107.10 4.90 1.40e+00 5.10e-01 1.23e+01 angle pdb=" C GLU A 613 " pdb=" N ASP A 614 " pdb=" CA ASP A 614 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 ... (remaining 9133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 3728 17.27 - 34.54: 316 34.54 - 51.80: 47 51.80 - 69.07: 6 69.07 - 86.34: 8 Dihedral angle restraints: 4105 sinusoidal: 1658 harmonic: 2447 Sorted by residual: dihedral pdb=" CA ARG A 643 " pdb=" C ARG A 643 " pdb=" N PRO A 644 " pdb=" CA PRO A 644 " ideal model delta harmonic sigma weight residual 180.00 -147.82 -32.18 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA LYS A1764 " pdb=" C LYS A1764 " pdb=" N ILE A1765 " pdb=" CA ILE A1765 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASP B 104 " pdb=" C ASP B 104 " pdb=" N THR B 105 " pdb=" CA THR B 105 " ideal model delta harmonic sigma weight residual 180.00 154.24 25.76 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 4102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 734 0.047 - 0.095: 220 0.095 - 0.142: 72 0.142 - 0.189: 2 0.189 - 0.237: 3 Chirality restraints: 1031 Sorted by residual: chirality pdb=" CB ILE A 640 " pdb=" CA ILE A 640 " pdb=" CG1 ILE A 640 " pdb=" CG2 ILE A 640 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PRO A 644 " pdb=" N PRO A 644 " pdb=" C PRO A 644 " pdb=" CB PRO A 644 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.88e-01 ... (remaining 1028 not shown) Planarity restraints: 1193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 643 " -0.092 5.00e-02 4.00e+02 1.39e-01 3.08e+01 pdb=" N PRO A 644 " 0.240 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 699 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C ASN A 699 " 0.033 2.00e-02 2.50e+03 pdb=" O ASN A 699 " -0.012 2.00e-02 2.50e+03 pdb=" N MET A 700 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 462 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C VAL A 462 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 462 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS A 463 " 0.011 2.00e-02 2.50e+03 ... (remaining 1190 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 188 2.70 - 3.25: 6969 3.25 - 3.80: 9773 3.80 - 4.35: 12870 4.35 - 4.90: 21155 Nonbonded interactions: 50955 Sorted by model distance: nonbonded pdb=" O ARG A1739 " pdb=" NZ LYS A1764 " model vdw 2.153 2.520 nonbonded pdb=" N GLY A1814 " pdb=" O TYR A1824 " model vdw 2.227 2.520 nonbonded pdb=" OD2 ASP B 89 " pdb=" OH TYR A1819 " model vdw 2.237 2.440 nonbonded pdb=" OD1 ASP A 423 " pdb=" OG1 THR A 426 " model vdw 2.243 2.440 nonbonded pdb=" O ASN A 699 " pdb=" ND2 ASN A 699 " model vdw 2.269 2.520 ... (remaining 50950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.590 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.430 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 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 : 0.003 0.060 6741 Z= 0.226 Angle : 0.735 13.681 9138 Z= 0.390 Chirality : 0.049 0.237 1031 Planarity : 0.006 0.139 1193 Dihedral : 13.271 86.339 2522 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.06 % Favored : 89.33 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.42 (0.30), residues: 825 helix: 0.74 (0.38), residues: 209 sheet: -1.64 (0.44), residues: 141 loop : -1.52 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 40 HIS 0.009 0.002 HIS B 69 PHE 0.030 0.002 PHE A1676 TYR 0.014 0.001 TYR A1661 ARG 0.002 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.816 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2019 time to fit residues: 38.6302 Evaluate side-chains 127 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6741 Z= 0.197 Angle : 0.664 12.575 9138 Z= 0.336 Chirality : 0.048 0.190 1031 Planarity : 0.005 0.132 1193 Dihedral : 6.056 31.159 894 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.48 % Favored : 91.03 % Rotamer: Outliers : 1.06 % Allowed : 7.57 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.43 (0.30), residues: 825 helix: 0.74 (0.37), residues: 213 sheet: -1.87 (0.43), residues: 141 loop : -1.47 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 520 HIS 0.003 0.001 HIS B 69 PHE 0.020 0.002 PHE A 780 TYR 0.017 0.002 TYR A1819 ARG 0.002 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 0.840 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 142 average time/residue: 0.2038 time to fit residues: 38.8941 Evaluate side-chains 135 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1266 time to fit residues: 2.2503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 25 optimal weight: 0.0000 chunk 60 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6741 Z= 0.168 Angle : 0.653 12.151 9138 Z= 0.323 Chirality : 0.047 0.183 1031 Planarity : 0.005 0.129 1193 Dihedral : 5.771 31.409 894 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.45 % Favored : 90.06 % Rotamer: Outliers : 1.33 % Allowed : 10.36 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.28 (0.30), residues: 825 helix: 0.89 (0.37), residues: 213 sheet: -2.04 (0.44), residues: 134 loop : -1.31 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 40 HIS 0.002 0.001 HIS B 69 PHE 0.009 0.001 PHE A 459 TYR 0.017 0.001 TYR A1819 ARG 0.001 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 0.706 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 143 average time/residue: 0.1910 time to fit residues: 36.4547 Evaluate side-chains 138 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0643 time to fit residues: 1.7722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6741 Z= 0.214 Angle : 0.677 12.951 9138 Z= 0.337 Chirality : 0.048 0.186 1031 Planarity : 0.005 0.127 1193 Dihedral : 5.904 31.546 894 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.33 % Favored : 90.18 % Rotamer: Outliers : 1.59 % Allowed : 12.62 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.30 (0.30), residues: 825 helix: 1.00 (0.38), residues: 208 sheet: -2.04 (0.42), residues: 140 loop : -1.35 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 37 HIS 0.002 0.001 HIS B 69 PHE 0.020 0.001 PHE A 780 TYR 0.015 0.002 TYR A1819 ARG 0.002 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 0.811 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 142 average time/residue: 0.1948 time to fit residues: 36.8562 Evaluate side-chains 140 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0729 time to fit residues: 1.9841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.0770 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 0.0170 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 0.0030 chunk 26 optimal weight: 0.7980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 6741 Z= 0.154 Angle : 0.633 10.310 9138 Z= 0.315 Chirality : 0.046 0.191 1031 Planarity : 0.005 0.124 1193 Dihedral : 5.494 31.344 894 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.88 % Favored : 91.64 % Rotamer: Outliers : 0.80 % Allowed : 14.48 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.22 (0.31), residues: 825 helix: 0.92 (0.38), residues: 214 sheet: -2.06 (0.43), residues: 134 loop : -1.25 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 37 HIS 0.002 0.001 HIS B 69 PHE 0.006 0.001 PHE B 16 TYR 0.011 0.001 TYR A1682 ARG 0.001 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 0.840 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 148 average time/residue: 0.1917 time to fit residues: 37.8506 Evaluate side-chains 137 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1963 time to fit residues: 2.7885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 0.1980 chunk 47 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 66 optimal weight: 0.0070 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.0270 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 6741 Z= 0.148 Angle : 0.618 10.189 9138 Z= 0.308 Chirality : 0.046 0.205 1031 Planarity : 0.005 0.123 1193 Dihedral : 5.259 31.433 894 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.12 % Favored : 91.39 % Rotamer: Outliers : 0.66 % Allowed : 16.07 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.08 (0.31), residues: 825 helix: 1.03 (0.38), residues: 208 sheet: -2.00 (0.43), residues: 134 loop : -1.13 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 37 HIS 0.002 0.001 HIS B 69 PHE 0.023 0.001 PHE A 780 TYR 0.013 0.001 TYR A1682 ARG 0.001 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 0.791 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 149 average time/residue: 0.1979 time to fit residues: 39.1159 Evaluate side-chains 139 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.775 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0658 time to fit residues: 1.2392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 6.9990 chunk 45 optimal weight: 0.0060 chunk 58 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1744 ASN A1870 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6741 Z= 0.164 Angle : 0.621 10.202 9138 Z= 0.310 Chirality : 0.046 0.203 1031 Planarity : 0.005 0.122 1193 Dihedral : 5.319 31.486 894 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.73 % Favored : 90.79 % Rotamer: Outliers : 1.33 % Allowed : 16.87 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.10 (0.31), residues: 825 helix: 0.95 (0.38), residues: 214 sheet: -2.04 (0.43), residues: 135 loop : -1.11 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 37 HIS 0.002 0.001 HIS B 69 PHE 0.007 0.001 PHE A 531 TYR 0.013 0.001 TYR A1803 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 0.927 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 143 average time/residue: 0.2083 time to fit residues: 39.3981 Evaluate side-chains 143 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0717 time to fit residues: 1.9405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 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 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6741 Z= 0.258 Angle : 0.703 10.444 9138 Z= 0.357 Chirality : 0.049 0.214 1031 Planarity : 0.005 0.123 1193 Dihedral : 5.982 31.758 894 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.94 % Favored : 89.58 % Rotamer: Outliers : 1.33 % Allowed : 16.73 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.38 (0.30), residues: 825 helix: 0.75 (0.38), residues: 214 sheet: -2.29 (0.42), residues: 135 loop : -1.28 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 761 HIS 0.002 0.001 HIS B 69 PHE 0.022 0.002 PHE A 780 TYR 0.016 0.002 TYR A1864 ARG 0.002 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 140 average time/residue: 0.2128 time to fit residues: 39.6115 Evaluate side-chains 134 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 0.838 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0712 time to fit residues: 1.5693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 70 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6741 Z= 0.184 Angle : 0.669 10.447 9138 Z= 0.336 Chirality : 0.047 0.205 1031 Planarity : 0.005 0.122 1193 Dihedral : 5.702 31.214 894 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.61 % Favored : 90.91 % Rotamer: Outliers : 0.13 % Allowed : 18.86 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.27 (0.30), residues: 825 helix: 1.07 (0.39), residues: 202 sheet: -2.20 (0.42), residues: 135 loop : -1.28 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 520 HIS 0.002 0.001 HIS B 69 PHE 0.014 0.001 PHE A 701 TYR 0.013 0.001 TYR A1803 ARG 0.001 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.824 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.1968 time to fit residues: 35.5563 Evaluate side-chains 132 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.754 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3415 time to fit residues: 1.4677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6741 Z= 0.190 Angle : 0.672 10.336 9138 Z= 0.337 Chirality : 0.047 0.187 1031 Planarity : 0.005 0.121 1193 Dihedral : 5.666 31.053 894 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.06 % Favored : 89.45 % Rotamer: Outliers : 0.66 % Allowed : 18.33 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.27 (0.31), residues: 825 helix: 1.08 (0.39), residues: 202 sheet: -2.22 (0.43), residues: 135 loop : -1.27 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 520 HIS 0.002 0.001 HIS B 69 PHE 0.023 0.001 PHE A 780 TYR 0.033 0.001 TYR A 742 ARG 0.001 0.000 ARG A 643 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 0.822 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 136 average time/residue: 0.2065 time to fit residues: 37.1239 Evaluate side-chains 133 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0674 time to fit residues: 1.6070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.211581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.198496 restraints weight = 8787.576| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 1.92 r_work: 0.4260 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6741 Z= 0.172 Angle : 0.664 10.322 9138 Z= 0.333 Chirality : 0.047 0.194 1031 Planarity : 0.005 0.120 1193 Dihedral : 5.534 30.712 894 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.09 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 18.73 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.15 (0.31), residues: 825 helix: 1.17 (0.39), residues: 202 sheet: -2.02 (0.44), residues: 132 loop : -1.25 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 520 HIS 0.008 0.001 HIS B 69 PHE 0.013 0.001 PHE A 701 TYR 0.012 0.001 TYR A1803 ARG 0.001 0.000 ARG B 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1872.86 seconds wall clock time: 34 minutes 32.90 seconds (2072.90 seconds total)