Starting phenix.real_space_refine on Sun Mar 10 19:47:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oof_17012/03_2024/8oof_17012_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oof_17012/03_2024/8oof_17012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oof_17012/03_2024/8oof_17012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oof_17012/03_2024/8oof_17012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oof_17012/03_2024/8oof_17012_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oof_17012/03_2024/8oof_17012_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 3 5.49 5 Mg 1 5.21 5 S 20 5.16 5 C 2837 2.51 5 N 799 2.21 5 O 819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ASP 620": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4479 Number of models: 1 Model: "" Number of chains: 2 Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 3606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3606 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'peptide': 447, 'undetermined': 2} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 418, None: 2} Not linked: pdbres="ALA J 767 " pdbres="ATP J 801 " Not linked: pdbres="ATP J 801 " pdbres=" MG J 802 " Chain breaks: 3 Time building chain proxies: 3.03, per 1000 atoms: 0.68 Number of scatterers: 4479 At special positions: 0 Unit cell: (89.598, 87.132, 85.488, 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 20 16.00 P 3 15.00 Mg 1 11.99 O 819 8.00 N 799 7.00 C 2837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 809.1 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 4 sheets defined 35.1% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'I' and resid 8 through 20 Processing helix chain 'I' and resid 44 through 51 Processing helix chain 'I' and resid 191 through 198 Processing helix chain 'I' and resid 204 through 212 removed outlier: 4.036A pdb=" N ARG I 212 " --> pdb=" O PHE I 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 51 Processing helix chain 'J' and resid 129 through 142 Processing helix chain 'J' and resid 166 through 178 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 225 through 227 No H-bonds generated for 'chain 'J' and resid 225 through 227' Processing helix chain 'J' and resid 235 through 249 Processing helix chain 'J' and resid 260 through 270 Processing helix chain 'J' and resid 277 through 282 Processing helix chain 'J' and resid 290 through 293 No H-bonds generated for 'chain 'J' and resid 290 through 293' Processing helix chain 'J' and resid 604 through 606 No H-bonds generated for 'chain 'J' and resid 604 through 606' Processing helix chain 'J' and resid 608 through 614 Processing helix chain 'J' and resid 633 through 638 removed outlier: 3.822A pdb=" N ARG J 638 " --> pdb=" O GLU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 642 No H-bonds generated for 'chain 'J' and resid 640 through 642' Processing helix chain 'J' and resid 646 through 649 No H-bonds generated for 'chain 'J' and resid 646 through 649' Processing helix chain 'J' and resid 657 through 666 Processing helix chain 'J' and resid 680 through 685 removed outlier: 4.429A pdb=" N ASP J 685 " --> pdb=" O ALA J 681 " (cutoff:3.500A) Processing helix chain 'J' and resid 691 through 693 No H-bonds generated for 'chain 'J' and resid 691 through 693' Processing helix chain 'J' and resid 698 through 707 Processing helix chain 'J' and resid 726 through 735 removed outlier: 3.691A pdb=" N GLY J 731 " --> pdb=" O ALA J 728 " (cutoff:3.500A) Processing helix chain 'J' and resid 739 through 742 No H-bonds generated for 'chain 'J' and resid 739 through 742' Processing helix chain 'J' and resid 748 through 754 removed outlier: 3.610A pdb=" N GLU J 753 " --> pdb=" O GLU J 749 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'J' and resid 27 through 29 removed outlier: 6.421A pdb=" N ILE J 296 " --> pdb=" O TYR J 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 80 through 82 removed outlier: 7.532A pdb=" N ILE J 61 " --> pdb=" O PRO J 155 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL J 157 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASN J 63 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR J 159 " --> pdb=" O ASN J 63 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 115 through 117 Processing sheet with id= D, first strand: chain 'J' and resid 213 through 218 128 hydrogen bonds defined for protein. 351 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: 1.23 Time building geometry restraints manager: 1.86 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: 1484 1.34 - 1.46: 727 1.46 - 1.57: 2346 1.57 - 1.69: 3 1.69 - 1.81: 34 Bond restraints: 4594 Sorted by residual: bond pdb=" CB THR J 689 " pdb=" CG2 THR J 689 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" CB LEU J 683 " pdb=" CG LEU J 683 " ideal model delta sigma weight residual 1.530 1.508 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" N ALA I 160 " pdb=" CA ALA I 160 " ideal model delta sigma weight residual 1.455 1.477 -0.022 2.40e-02 1.74e+03 8.12e-01 bond pdb=" CG ARG J 636 " pdb=" CD ARG J 636 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.03e-01 bond pdb=" O3B ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 1.592 1.566 0.026 3.00e-02 1.11e+03 7.49e-01 ... (remaining 4589 not shown) Histogram of bond angle deviations from ideal: 99.74 - 107.72: 248 107.72 - 115.69: 2706 115.69 - 123.67: 3095 123.67 - 131.64: 170 131.64 - 139.62: 14 Bond angle restraints: 6233 Sorted by residual: angle pdb=" CA GLU J 17 " pdb=" C GLU J 17 " pdb=" N PRO J 18 " ideal model delta sigma weight residual 116.90 121.49 -4.59 1.50e+00 4.44e-01 9.35e+00 angle pdb=" N THR J 627 " pdb=" CA THR J 627 " pdb=" C THR J 627 " ideal model delta sigma weight residual 110.19 107.25 2.94 1.24e+00 6.50e-01 5.61e+00 angle pdb=" N VAL J 634 " pdb=" CA VAL J 634 " pdb=" C VAL J 634 " ideal model delta sigma weight residual 111.05 113.96 -2.91 1.25e+00 6.40e-01 5.41e+00 angle pdb=" N ALA I 160 " pdb=" CA ALA I 160 " pdb=" C ALA I 160 " ideal model delta sigma weight residual 107.37 114.11 -6.74 2.96e+00 1.14e-01 5.19e+00 angle pdb=" CA ARG J 295 " pdb=" CB ARG J 295 " pdb=" CG ARG J 295 " ideal model delta sigma weight residual 114.10 109.68 4.42 2.00e+00 2.50e-01 4.88e+00 ... (remaining 6228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 2518 16.44 - 32.88: 187 32.88 - 49.32: 51 49.32 - 65.76: 8 65.76 - 82.20: 6 Dihedral angle restraints: 2770 sinusoidal: 1160 harmonic: 1610 Sorted by residual: dihedral pdb=" CA GLU J 626 " pdb=" C GLU J 626 " pdb=" N THR J 627 " pdb=" CA THR J 627 " ideal model delta harmonic sigma weight residual 180.00 150.59 29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASP J 104 " pdb=" C ASP J 104 " pdb=" N CYS J 105 " pdb=" CA CYS J 105 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ARG J 90 " pdb=" C ARG J 90 " pdb=" N ASP J 91 " pdb=" CA ASP J 91 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 2767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 417 0.041 - 0.083: 170 0.083 - 0.124: 62 0.124 - 0.165: 2 0.165 - 0.206: 3 Chirality restraints: 654 Sorted by residual: chirality pdb=" CB ILE J 39 " pdb=" CA ILE J 39 " pdb=" CG1 ILE J 39 " pdb=" CG2 ILE J 39 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA GLU J 635 " pdb=" N GLU J 635 " pdb=" C GLU J 635 " pdb=" CB GLU J 635 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA ARG I 185 " pdb=" N ARG I 185 " pdb=" C ARG I 185 " pdb=" CB ARG I 185 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 651 not shown) Planarity restraints: 811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 293 " -0.210 9.50e-02 1.11e+02 9.48e-02 6.86e+00 pdb=" NE ARG J 293 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG J 293 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG J 293 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG J 293 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 284 " -0.007 2.00e-02 2.50e+03 1.46e-02 4.28e+00 pdb=" CG TYR J 284 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR J 284 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR J 284 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 284 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR J 284 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR J 284 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR J 284 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 636 " 0.165 9.50e-02 1.11e+02 7.45e-02 4.03e+00 pdb=" NE ARG J 636 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG J 636 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG J 636 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG J 636 " 0.001 2.00e-02 2.50e+03 ... (remaining 808 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 35 2.61 - 3.19: 4007 3.19 - 3.76: 6821 3.76 - 4.33: 10180 4.33 - 4.90: 16185 Nonbonded interactions: 37228 Sorted by model distance: nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 802 " model vdw 2.043 2.170 nonbonded pdb=" O1B ATP J 801 " pdb="MG MG J 802 " model vdw 2.087 2.170 nonbonded pdb=" O1G ATP J 801 " pdb="MG MG J 802 " model vdw 2.096 2.170 nonbonded pdb=" OE2 GLU J 264 " pdb=" NH2 ARG J 268 " model vdw 2.231 2.520 nonbonded pdb=" NZ LYS I 42 " pdb=" OE1 GLU I 50 " model vdw 2.305 2.520 ... (remaining 37223 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: 1.920 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: 9.290 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.770 Find NCS groups from input model: 0.110 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:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.004 0.043 4594 Z= 0.276 Angle : 0.706 6.743 6233 Z= 0.407 Chirality : 0.049 0.206 654 Planarity : 0.009 0.095 811 Dihedral : 13.651 82.195 1734 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.34), residues: 544 helix: -1.27 (0.33), residues: 197 sheet: 0.92 (0.80), residues: 46 loop : -0.10 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 735 HIS 0.008 0.002 HIS J 197 PHE 0.019 0.002 PHE J 612 TYR 0.023 0.004 TYR J 284 ARG 0.021 0.003 ARG J 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: I 48 LEU cc_start: 0.8993 (mt) cc_final: 0.8675 (mt) REVERT: I 191 LYS cc_start: 0.8398 (pttt) cc_final: 0.7010 (mmtt) REVERT: J 677 ASP cc_start: 0.7923 (t0) cc_final: 0.7552 (t0) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 1.5303 time to fit residues: 155.9774 Evaluate side-chains 67 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.0770 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4594 Z= 0.184 Angle : 0.542 5.443 6233 Z= 0.284 Chirality : 0.042 0.128 654 Planarity : 0.005 0.040 811 Dihedral : 7.813 81.482 649 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.93 % Allowed : 11.35 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.35), residues: 544 helix: 0.35 (0.35), residues: 210 sheet: 0.50 (0.84), residues: 47 loop : 0.51 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 129 HIS 0.004 0.001 HIS J 197 PHE 0.011 0.001 PHE J 612 TYR 0.009 0.001 TYR J 167 ARG 0.004 0.000 ARG J 748 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.533 Fit side-chains REVERT: I 42 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7882 (mtmt) REVERT: I 48 LEU cc_start: 0.9036 (mt) cc_final: 0.8759 (mt) REVERT: I 158 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6704 (mt-10) REVERT: I 191 LYS cc_start: 0.8405 (pttt) cc_final: 0.7025 (mmpt) REVERT: J 98 PHE cc_start: 0.8770 (m-80) cc_final: 0.8521 (m-10) REVERT: J 677 ASP cc_start: 0.8095 (t0) cc_final: 0.7869 (t0) outliers start: 9 outliers final: 3 residues processed: 78 average time/residue: 1.4556 time to fit residues: 117.2424 Evaluate side-chains 66 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.0170 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 73 ASN J 628 HIS J 654 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4594 Z= 0.198 Angle : 0.519 5.496 6233 Z= 0.269 Chirality : 0.042 0.127 654 Planarity : 0.005 0.046 811 Dihedral : 7.491 81.135 649 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.00 % Allowed : 12.42 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.36), residues: 544 helix: 0.89 (0.37), residues: 201 sheet: 0.38 (0.79), residues: 52 loop : 0.60 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 287 HIS 0.003 0.001 HIS J 762 PHE 0.011 0.001 PHE J 612 TYR 0.008 0.001 TYR J 180 ARG 0.008 0.000 ARG J 748 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.530 Fit side-chains REVERT: I 42 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7886 (mtmt) REVERT: I 48 LEU cc_start: 0.9034 (mt) cc_final: 0.8749 (mt) REVERT: I 158 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6676 (mt-10) REVERT: I 191 LYS cc_start: 0.8373 (pttt) cc_final: 0.7054 (mmtt) REVERT: J 98 PHE cc_start: 0.8760 (m-80) cc_final: 0.8527 (m-10) REVERT: J 242 MET cc_start: 0.8900 (tpp) cc_final: 0.8670 (tpp) REVERT: J 626 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: J 677 ASP cc_start: 0.8155 (t0) cc_final: 0.7929 (t0) outliers start: 14 outliers final: 5 residues processed: 74 average time/residue: 1.4900 time to fit residues: 113.7791 Evaluate side-chains 70 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 257 LYS Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.0050 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4594 Z= 0.241 Angle : 0.528 5.269 6233 Z= 0.273 Chirality : 0.043 0.128 654 Planarity : 0.004 0.044 811 Dihedral : 7.454 80.233 649 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.00 % Allowed : 12.42 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.36), residues: 544 helix: 0.85 (0.36), residues: 207 sheet: 0.16 (0.77), residues: 52 loop : 0.50 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 129 HIS 0.003 0.001 HIS I 189 PHE 0.012 0.002 PHE J 612 TYR 0.011 0.001 TYR J 180 ARG 0.002 0.000 ARG I 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.564 Fit side-chains REVERT: I 42 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7868 (mtmt) REVERT: I 48 LEU cc_start: 0.9026 (mt) cc_final: 0.8755 (mt) REVERT: I 191 LYS cc_start: 0.8411 (pttt) cc_final: 0.7067 (mmtt) REVERT: J 48 ARG cc_start: 0.7595 (mtt-85) cc_final: 0.7341 (mtp180) REVERT: J 98 PHE cc_start: 0.8779 (m-80) cc_final: 0.8551 (m-10) REVERT: J 677 ASP cc_start: 0.8172 (t0) cc_final: 0.7878 (t0) outliers start: 14 outliers final: 8 residues processed: 68 average time/residue: 1.3941 time to fit residues: 98.0669 Evaluate side-chains 69 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 257 LYS Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.0020 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4594 Z= 0.245 Angle : 0.519 5.287 6233 Z= 0.268 Chirality : 0.043 0.125 654 Planarity : 0.004 0.042 811 Dihedral : 7.383 80.806 649 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.78 % Allowed : 13.49 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.35), residues: 544 helix: 1.16 (0.36), residues: 201 sheet: -0.10 (0.77), residues: 46 loop : 0.37 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 287 HIS 0.003 0.001 HIS J 762 PHE 0.012 0.002 PHE J 612 TYR 0.010 0.001 TYR J 180 ARG 0.002 0.000 ARG J 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.554 Fit side-chains REVERT: I 42 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7860 (mtmt) REVERT: I 48 LEU cc_start: 0.9033 (mt) cc_final: 0.8758 (mt) REVERT: I 191 LYS cc_start: 0.8413 (pttt) cc_final: 0.7083 (mmtt) REVERT: J 98 PHE cc_start: 0.8794 (m-80) cc_final: 0.8536 (m-10) REVERT: J 242 MET cc_start: 0.8871 (tpp) cc_final: 0.8671 (tpp) REVERT: J 677 ASP cc_start: 0.8253 (t0) cc_final: 0.8008 (t0) outliers start: 13 outliers final: 7 residues processed: 70 average time/residue: 1.4273 time to fit residues: 103.3556 Evaluate side-chains 67 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 257 LYS Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.0370 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 73 ASN J 237 HIS J 697 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4594 Z= 0.231 Angle : 0.507 5.250 6233 Z= 0.262 Chirality : 0.042 0.124 654 Planarity : 0.004 0.044 811 Dihedral : 7.275 81.297 649 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.43 % Allowed : 13.49 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.36), residues: 544 helix: 1.24 (0.37), residues: 201 sheet: -0.12 (0.77), residues: 46 loop : 0.33 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 287 HIS 0.003 0.001 HIS J 628 PHE 0.010 0.001 PHE J 612 TYR 0.008 0.001 TYR J 210 ARG 0.003 0.000 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.541 Fit side-chains REVERT: I 42 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7896 (mtmt) REVERT: I 48 LEU cc_start: 0.9033 (mt) cc_final: 0.8759 (mt) REVERT: I 191 LYS cc_start: 0.8405 (pttt) cc_final: 0.7067 (mmtt) REVERT: J 48 ARG cc_start: 0.7626 (mtt-85) cc_final: 0.7423 (mtp180) REVERT: J 677 ASP cc_start: 0.8254 (t0) cc_final: 0.8004 (t0) outliers start: 16 outliers final: 10 residues processed: 72 average time/residue: 1.3453 time to fit residues: 100.2806 Evaluate side-chains 71 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.0370 chunk 43 optimal weight: 0.0060 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 33 optimal weight: 0.3980 overall best weight: 0.1652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 73 ASN J 722 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4594 Z= 0.140 Angle : 0.459 5.156 6233 Z= 0.236 Chirality : 0.040 0.123 654 Planarity : 0.004 0.038 811 Dihedral : 6.697 84.963 649 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.57 % Allowed : 15.20 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.36), residues: 544 helix: 1.29 (0.37), residues: 207 sheet: -0.12 (0.77), residues: 46 loop : 0.46 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 129 HIS 0.003 0.001 HIS J 628 PHE 0.013 0.001 PHE J 98 TYR 0.007 0.001 TYR J 272 ARG 0.001 0.000 ARG J 617 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.569 Fit side-chains REVERT: I 42 LYS cc_start: 0.8153 (mtmt) cc_final: 0.7896 (mtmt) REVERT: I 48 LEU cc_start: 0.9005 (mt) cc_final: 0.8728 (mt) REVERT: I 191 LYS cc_start: 0.8384 (pttt) cc_final: 0.7058 (mmtt) REVERT: I 206 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7817 (mm-30) REVERT: J 677 ASP cc_start: 0.8290 (t0) cc_final: 0.8018 (t0) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 1.3340 time to fit residues: 94.0231 Evaluate side-chains 65 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 73 ASN Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4594 Z= 0.214 Angle : 0.492 5.200 6233 Z= 0.251 Chirality : 0.042 0.124 654 Planarity : 0.004 0.038 811 Dihedral : 6.954 82.351 649 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.00 % Allowed : 15.42 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.36), residues: 544 helix: 1.37 (0.37), residues: 201 sheet: -0.10 (0.78), residues: 46 loop : 0.41 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 287 HIS 0.003 0.001 HIS J 762 PHE 0.019 0.002 PHE J 98 TYR 0.008 0.001 TYR J 180 ARG 0.002 0.000 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.530 Fit side-chains REVERT: I 35 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6770 (mtm-85) REVERT: I 42 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7855 (mtmt) REVERT: I 48 LEU cc_start: 0.9015 (mt) cc_final: 0.8742 (mt) REVERT: I 191 LYS cc_start: 0.8408 (pttt) cc_final: 0.7072 (mmtt) REVERT: J 677 ASP cc_start: 0.8306 (t0) cc_final: 0.8065 (t0) outliers start: 14 outliers final: 9 residues processed: 68 average time/residue: 1.3888 time to fit residues: 97.7477 Evaluate side-chains 69 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.0020 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4594 Z= 0.236 Angle : 0.542 8.265 6233 Z= 0.275 Chirality : 0.042 0.124 654 Planarity : 0.004 0.049 811 Dihedral : 7.121 81.760 649 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.00 % Allowed : 15.63 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.36), residues: 544 helix: 1.22 (0.37), residues: 201 sheet: -0.09 (0.77), residues: 46 loop : 0.33 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 287 HIS 0.003 0.001 HIS J 628 PHE 0.018 0.001 PHE J 98 TYR 0.008 0.001 TYR I 188 ARG 0.002 0.000 ARG J 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.550 Fit side-chains REVERT: I 35 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6780 (mtm-85) REVERT: I 42 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7853 (mtmt) REVERT: I 48 LEU cc_start: 0.9025 (mt) cc_final: 0.8754 (mt) REVERT: I 191 LYS cc_start: 0.8408 (pttt) cc_final: 0.7087 (mmtt) outliers start: 14 outliers final: 9 residues processed: 70 average time/residue: 1.6675 time to fit residues: 120.4392 Evaluate side-chains 69 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 45 optimal weight: 0.0040 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4594 Z= 0.215 Angle : 0.531 8.125 6233 Z= 0.272 Chirality : 0.042 0.143 654 Planarity : 0.004 0.048 811 Dihedral : 7.011 82.925 649 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.14 % Allowed : 16.27 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.35), residues: 544 helix: 1.15 (0.37), residues: 201 sheet: -0.01 (0.77), residues: 46 loop : 0.28 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 287 HIS 0.003 0.001 HIS J 762 PHE 0.009 0.001 PHE J 612 TYR 0.008 0.001 TYR J 210 ARG 0.003 0.000 ARG J 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.539 Fit side-chains REVERT: I 35 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6812 (mtm-85) REVERT: I 42 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7859 (mtmt) REVERT: I 48 LEU cc_start: 0.9027 (mt) cc_final: 0.8765 (mt) REVERT: I 191 LYS cc_start: 0.8406 (pttt) cc_final: 0.7082 (mmtt) REVERT: J 39 ILE cc_start: 0.7275 (pp) cc_final: 0.6750 (pt) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 1.5195 time to fit residues: 103.5355 Evaluate side-chains 67 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 35 ARG Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.089794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.072508 restraints weight = 7581.607| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.81 r_work: 0.2974 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4594 Z= 0.252 Angle : 0.547 7.332 6233 Z= 0.281 Chirality : 0.042 0.141 654 Planarity : 0.004 0.049 811 Dihedral : 7.203 81.348 649 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.14 % Allowed : 16.70 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.35), residues: 544 helix: 1.05 (0.37), residues: 201 sheet: -0.04 (0.77), residues: 46 loop : 0.16 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 287 HIS 0.003 0.001 HIS J 762 PHE 0.010 0.001 PHE J 612 TYR 0.009 0.001 TYR J 180 ARG 0.003 0.000 ARG J 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2526.66 seconds wall clock time: 45 minutes 3.71 seconds (2703.71 seconds total)