Starting phenix.real_space_refine on Fri Dec 8 03:46:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swf_25472/12_2023/7swf_25472.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swf_25472/12_2023/7swf_25472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swf_25472/12_2023/7swf_25472.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swf_25472/12_2023/7swf_25472.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swf_25472/12_2023/7swf_25472.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swf_25472/12_2023/7swf_25472.pdb" } resolution = 3.79 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 34 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 4227 2.51 5 N 1214 2.21 5 O 1361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 821": "OE1" <-> "OE2" Residue "A PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6873 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6167 Classifications: {'peptide': 778} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 43, 'TRANS': 734} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 370 Classifications: {'RNA': 17} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "D" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 335 Classifications: {'DNA': 1, 'RNA': 16} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 15} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.53, per 1000 atoms: 0.66 Number of scatterers: 6873 At special positions: 0 Unit cell: (80.99, 101.92, 114.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 34 15.00 Mg 1 11.99 O 1361 8.00 N 1214 7.00 C 4227 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: 3.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 11 sheets defined 31.9% alpha, 10.3% beta 15 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 263 through 283 removed outlier: 3.521A pdb=" N ALA A 267 " --> pdb=" O CYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 460 through 472 removed outlier: 3.806A pdb=" N ALA A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 removed outlier: 3.917A pdb=" N VAL A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 565 through 584 Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 636 through 648 removed outlier: 4.212A pdb=" N GLU A 646 " --> pdb=" O LYS A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 663 Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.826A pdb=" N LYS A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 801 through 819 Processing helix chain 'A' and resid 903 through 915 Processing helix chain 'A' and resid 928 through 941 removed outlier: 4.038A pdb=" N ALA A 934 " --> pdb=" O PRO A 930 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HIS A 935 " --> pdb=" O ALA A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 945 removed outlier: 3.791A pdb=" N LEU A 945 " --> pdb=" O ARG A 942 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 945' Processing helix chain 'A' and resid 978 through 982 Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA2, first strand: chain 'A' and resid 314 through 316 removed outlier: 3.590A pdb=" N SER A 314 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 197 Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 300 removed outlier: 3.727A pdb=" N GLN A 299 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374 Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 390 removed outlier: 4.042A pdb=" N SER A 440 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.563A pdb=" N LEU A 521 " --> pdb=" O CYS A 532 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 686 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 596 through 597 removed outlier: 7.008A pdb=" N ALA A 556 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 629 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL A 558 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 703 through 705 removed outlier: 5.994A pdb=" N ILE A 704 " --> pdb=" O ILE A 791 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 828 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP A 898 " --> pdb=" O VAL A 828 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE A 830 " --> pdb=" O LEU A 896 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 707 through 711 removed outlier: 3.623A pdb=" N ILE A 723 " --> pdb=" O THR A 711 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 722 " --> pdb=" O GLN A 745 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 759 through 761 removed outlier: 3.707A pdb=" N TRP A 759 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 767 " --> pdb=" O TRP A 759 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1751 1.33 - 1.45: 1422 1.45 - 1.57: 3794 1.57 - 1.69: 66 1.69 - 1.81: 50 Bond restraints: 7083 Sorted by residual: bond pdb=" N VAL A 173 " pdb=" CA VAL A 173 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.80e+00 bond pdb=" N VAL A 286 " pdb=" CA VAL A 286 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.80e+00 bond pdb=" N ARG A 288 " pdb=" CA ARG A 288 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.50e+00 bond pdb=" N ILE A 178 " pdb=" CA ILE A 178 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.19e-02 7.06e+03 6.35e+00 bond pdb=" N VAL A 182 " pdb=" CA VAL A 182 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.17e-02 7.31e+03 6.26e+00 ... (remaining 7078 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.56: 315 105.56 - 112.67: 3813 112.67 - 119.78: 2322 119.78 - 126.89: 3140 126.89 - 134.00: 154 Bond angle restraints: 9744 Sorted by residual: angle pdb=" C3' C D 7 " pdb=" O3' C D 7 " pdb=" P A D 8 " ideal model delta sigma weight residual 120.20 110.77 9.43 1.50e+00 4.44e-01 3.95e+01 angle pdb=" C3' U D 9 " pdb=" O3' U D 9 " pdb=" P U D 10 " ideal model delta sigma weight residual 120.20 113.70 6.50 1.50e+00 4.44e-01 1.88e+01 angle pdb=" CA ARG A 836 " pdb=" C ARG A 836 " pdb=" O ARG A 836 " ideal model delta sigma weight residual 122.64 118.36 4.28 1.25e+00 6.40e-01 1.17e+01 angle pdb=" C THR A 711 " pdb=" CA THR A 711 " pdb=" CB THR A 711 " ideal model delta sigma weight residual 111.23 115.95 -4.72 1.42e+00 4.96e-01 1.11e+01 angle pdb=" CA HIS A 837 " pdb=" C HIS A 837 " pdb=" O HIS A 837 " ideal model delta sigma weight residual 121.16 117.41 3.75 1.13e+00 7.83e-01 1.10e+01 ... (remaining 9739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 4170 35.68 - 71.36: 133 71.36 - 107.03: 14 107.03 - 142.71: 0 142.71 - 178.39: 2 Dihedral angle restraints: 4319 sinusoidal: 2048 harmonic: 2271 Sorted by residual: dihedral pdb=" C4' C D 20 " pdb=" C3' C D 20 " pdb=" O3' C D 20 " pdb=" P A D 21 " ideal model delta sinusoidal sigma weight residual -140.00 38.39 -178.39 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA SER A 855 " pdb=" C SER A 855 " pdb=" N GLY A 856 " pdb=" CA GLY A 856 " ideal model delta harmonic sigma weight residual 180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA MET A 320 " pdb=" C MET A 320 " pdb=" N GLY A 321 " pdb=" CA GLY A 321 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 4316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1019 0.086 - 0.171: 92 0.171 - 0.257: 3 0.257 - 0.343: 0 0.343 - 0.429: 2 Chirality restraints: 1116 Sorted by residual: chirality pdb=" P A D 8 " pdb=" OP1 A D 8 " pdb=" OP2 A D 8 " pdb=" O5' A D 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.84 -0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" P U D 9 " pdb=" OP1 U D 9 " pdb=" OP2 U D 9 " pdb=" O5' U D 9 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA ILE A 177 " pdb=" N ILE A 177 " pdb=" C ILE A 177 " pdb=" CB ILE A 177 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1113 not shown) Planarity restraints: 1132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 169 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C SER A 169 " -0.039 2.00e-02 2.50e+03 pdb=" O SER A 169 " 0.015 2.00e-02 2.50e+03 pdb=" N SER A 170 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 6 " 0.020 2.00e-02 2.50e+03 1.07e-02 2.57e+00 pdb=" N1 U B 6 " -0.024 2.00e-02 2.50e+03 pdb=" C2 U B 6 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U B 6 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U B 6 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U B 6 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U B 6 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U B 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 6 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 929 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 930 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 930 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 930 " 0.022 5.00e-02 4.00e+02 ... (remaining 1129 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 94 2.61 - 3.18: 6083 3.18 - 3.76: 10865 3.76 - 4.33: 14065 4.33 - 4.90: 23025 Nonbonded interactions: 54132 Sorted by model distance: nonbonded pdb=" OP1 U D 12 " pdb="MG MG A1001 " model vdw 2.039 2.170 nonbonded pdb=" OD2 ASP A 709 " pdb="MG MG A1001 " model vdw 2.044 2.170 nonbonded pdb=" OD1 ASP A 709 " pdb="MG MG A1001 " model vdw 2.096 2.170 nonbonded pdb=" O VAL A 470 " pdb=" NE2 GLN A 473 " model vdw 2.176 2.520 nonbonded pdb=" OG1 THR A 852 " pdb=" O ARG A 854 " model vdw 2.187 2.440 ... (remaining 54127 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 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: 0.330 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: 0.010 Extract box with map and model: 2.060 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.570 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.005 0.057 7083 Z= 0.334 Angle : 0.726 9.427 9744 Z= 0.415 Chirality : 0.049 0.429 1116 Planarity : 0.004 0.038 1132 Dihedral : 16.719 178.388 2851 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.33 % Allowed : 0.88 % Favored : 97.79 % 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: -1.82 (0.31), residues: 768 helix: 1.31 (0.36), residues: 230 sheet: -2.83 (0.42), residues: 131 loop : -2.21 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 308 HIS 0.004 0.001 HIS A 837 PHE 0.018 0.002 PHE A 802 TYR 0.017 0.002 TYR A 312 ARG 0.003 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.853 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 94 average time/residue: 0.2599 time to fit residues: 30.9293 Evaluate side-chains 67 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0724 time to fit residues: 1.5533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 40 optimal weight: 0.0170 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 23 optimal weight: 40.0000 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN A 760 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7083 Z= 0.207 Angle : 0.596 7.911 9744 Z= 0.294 Chirality : 0.041 0.188 1116 Planarity : 0.004 0.037 1132 Dihedral : 14.501 175.934 1324 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.77 % Allowed : 11.78 % Favored : 86.45 % 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: -1.54 (0.31), residues: 768 helix: 1.72 (0.36), residues: 232 sheet: -2.66 (0.39), residues: 156 loop : -2.10 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 732 HIS 0.003 0.001 HIS A 488 PHE 0.012 0.001 PHE A 874 TYR 0.020 0.001 TYR A 185 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.754 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 81 average time/residue: 0.2069 time to fit residues: 22.5758 Evaluate side-chains 69 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.677 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0631 time to fit residues: 1.7555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 40.0000 chunk 57 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN A 857 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7083 Z= 0.423 Angle : 0.703 13.277 9744 Z= 0.350 Chirality : 0.044 0.220 1116 Planarity : 0.005 0.051 1132 Dihedral : 14.626 174.981 1324 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 2.21 % Allowed : 15.02 % Favored : 82.77 % 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: -1.57 (0.31), residues: 768 helix: 1.52 (0.35), residues: 233 sheet: -2.49 (0.41), residues: 153 loop : -2.10 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 732 HIS 0.006 0.001 HIS A 609 PHE 0.015 0.002 PHE A 874 TYR 0.013 0.002 TYR A 312 ARG 0.003 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.799 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 75 average time/residue: 0.2582 time to fit residues: 25.7424 Evaluate side-chains 67 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0830 time to fit residues: 3.2521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7083 Z= 0.183 Angle : 0.597 9.960 9744 Z= 0.292 Chirality : 0.040 0.211 1116 Planarity : 0.004 0.046 1132 Dihedral : 14.515 173.798 1324 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.91 % Allowed : 15.91 % Favored : 82.18 % 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: -1.34 (0.31), residues: 768 helix: 1.95 (0.36), residues: 231 sheet: -2.40 (0.41), residues: 148 loop : -2.11 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 897 HIS 0.003 0.001 HIS A 712 PHE 0.009 0.001 PHE A 874 TYR 0.016 0.001 TYR A 987 ARG 0.004 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.800 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 82 average time/residue: 0.2423 time to fit residues: 26.0138 Evaluate side-chains 67 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0649 time to fit residues: 1.7066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 0.0000 chunk 19 optimal weight: 0.0870 chunk 25 optimal weight: 0.0170 chunk 15 optimal weight: 3.9990 chunk 44 optimal weight: 0.0010 overall best weight: 0.1606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 GLN A 671 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7083 Z= 0.142 Angle : 0.568 8.653 9744 Z= 0.273 Chirality : 0.039 0.144 1116 Planarity : 0.004 0.041 1132 Dihedral : 14.450 174.317 1324 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.33 % Allowed : 18.41 % Favored : 80.27 % 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 (0.31), residues: 768 helix: 2.08 (0.36), residues: 233 sheet: -2.33 (0.41), residues: 151 loop : -2.08 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 732 HIS 0.002 0.000 HIS A 712 PHE 0.007 0.001 PHE A 986 TYR 0.015 0.001 TYR A 987 ARG 0.003 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.710 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 80 average time/residue: 0.2031 time to fit residues: 22.0882 Evaluate side-chains 63 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0673 time to fit residues: 1.2556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN A 667 GLN A 671 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7083 Z= 0.371 Angle : 0.689 12.249 9744 Z= 0.339 Chirality : 0.043 0.164 1116 Planarity : 0.005 0.054 1132 Dihedral : 14.495 174.726 1324 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 2.36 % Allowed : 18.26 % Favored : 79.38 % 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: -1.25 (0.31), residues: 768 helix: 1.90 (0.36), residues: 231 sheet: -2.32 (0.41), residues: 153 loop : -1.95 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 308 HIS 0.006 0.001 HIS A 609 PHE 0.012 0.001 PHE A 874 TYR 0.013 0.002 TYR A 185 ARG 0.006 0.000 ARG A 794 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 67 average time/residue: 0.1907 time to fit residues: 17.9894 Evaluate side-chains 59 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0753 time to fit residues: 2.2659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7083 Z= 0.195 Angle : 0.625 11.448 9744 Z= 0.299 Chirality : 0.041 0.166 1116 Planarity : 0.004 0.054 1132 Dihedral : 14.474 173.962 1324 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.18 % Allowed : 20.03 % Favored : 78.79 % 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: -1.29 (0.31), residues: 768 helix: 1.92 (0.36), residues: 235 sheet: -2.35 (0.41), residues: 148 loop : -2.08 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 732 HIS 0.002 0.001 HIS A 488 PHE 0.008 0.001 PHE A 874 TYR 0.012 0.001 TYR A 185 ARG 0.005 0.000 ARG A 794 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.797 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.1987 time to fit residues: 19.3344 Evaluate side-chains 62 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0696 time to fit residues: 1.5847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 37 optimal weight: 0.0070 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 671 ASN ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7083 Z= 0.154 Angle : 0.628 12.038 9744 Z= 0.296 Chirality : 0.040 0.191 1116 Planarity : 0.004 0.055 1132 Dihedral : 14.447 174.408 1324 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.74 % Allowed : 21.50 % Favored : 77.76 % 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: -1.05 (0.31), residues: 768 helix: 2.07 (0.36), residues: 233 sheet: -1.77 (0.46), residues: 124 loop : -2.11 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 732 HIS 0.001 0.000 HIS A 147 PHE 0.006 0.001 PHE A 572 TYR 0.012 0.001 TYR A 185 ARG 0.005 0.000 ARG A 794 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.897 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.2002 time to fit residues: 20.4845 Evaluate side-chains 66 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0701 time to fit residues: 1.5422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7083 Z= 0.292 Angle : 0.661 9.905 9744 Z= 0.317 Chirality : 0.042 0.181 1116 Planarity : 0.004 0.047 1132 Dihedral : 14.450 174.327 1324 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.88 % Allowed : 21.80 % Favored : 77.32 % 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: -1.22 (0.30), residues: 768 helix: 1.91 (0.36), residues: 236 sheet: -2.17 (0.46), residues: 117 loop : -2.13 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 732 HIS 0.004 0.001 HIS A 609 PHE 0.010 0.001 PHE A 874 TYR 0.011 0.001 TYR A 312 ARG 0.007 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.694 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 65 average time/residue: 0.1814 time to fit residues: 16.6466 Evaluate side-chains 59 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0673 time to fit residues: 1.3200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 19 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7083 Z= 0.178 Angle : 0.643 12.661 9744 Z= 0.302 Chirality : 0.040 0.176 1116 Planarity : 0.004 0.047 1132 Dihedral : 14.430 174.260 1324 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.29 % Allowed : 22.83 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.31), residues: 768 helix: 2.03 (0.36), residues: 234 sheet: -1.92 (0.47), residues: 113 loop : -2.10 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 732 HIS 0.002 0.001 HIS A 712 PHE 0.006 0.001 PHE A 290 TYR 0.012 0.001 TYR A 185 ARG 0.007 0.000 ARG A 694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.774 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 0.1731 time to fit residues: 16.2806 Evaluate side-chains 62 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.679 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0777 time to fit residues: 1.0883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.116500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.078431 restraints weight = 16154.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.080840 restraints weight = 7622.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.082295 restraints weight = 4848.040| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7083 Z= 0.301 Angle : 0.668 11.898 9744 Z= 0.321 Chirality : 0.042 0.175 1116 Planarity : 0.004 0.055 1132 Dihedral : 14.426 173.945 1324 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.59 % Allowed : 22.97 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.31), residues: 768 helix: 1.98 (0.36), residues: 231 sheet: -2.16 (0.45), residues: 129 loop : -1.97 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 759 HIS 0.004 0.001 HIS A 609 PHE 0.012 0.001 PHE A 874 TYR 0.010 0.001 TYR A 312 ARG 0.007 0.000 ARG A 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.30 seconds wall clock time: 28 minutes 3.47 seconds (1683.47 seconds total)