Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 17:24:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oof_17012/08_2023/8oof_17012_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oof_17012/08_2023/8oof_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_17012/08_2023/8oof_17012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oof_17012/08_2023/8oof_17012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oof_17012/08_2023/8oof_17012_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oof_17012/08_2023/8oof_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-1.21rc1-5044/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: 2.52, per 1000 atoms: 0.56 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: 1.87 Conformation dependent library (CDL) restraints added in 586.9 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: 0.85 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: 1.09 Time building geometry restraints manager: 2.02 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: 2509 16.44 - 32.88: 180 32.88 - 49.32: 38 49.32 - 65.76: 6 65.76 - 82.20: 6 Dihedral angle restraints: 2739 sinusoidal: 1129 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 2736 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: 1.900 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: 9.400 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 15.810 Find NCS groups from input model: 0.130 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:10.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 38.270 ------------------------------------------------------------------------------- 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 : 12.988 82.195 1703 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 % 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 *********************** 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 : 0.521 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 1.5464 time to fit residues: 157.5839 Evaluate side-chains 65 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7557 ------------------------------------------------------------------------------- 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: 0.0870 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: 0.2514 ------------------------------------------------------------------------------- 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 J 654 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 4594 Z= 0.163 Angle : 0.534 5.345 6233 Z= 0.279 Chirality : 0.042 0.128 654 Planarity : 0.004 0.039 811 Dihedral : 6.493 83.526 618 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 2.14 % 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: 0.48 (0.35), residues: 544 helix: 0.33 (0.36), residues: 210 sheet: 0.72 (0.88), residues: 41 loop : 0.42 (0.35), residues: 293 *********************** 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: 10 poor density : 73 time to evaluate : 0.544 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 78 average time/residue: 1.4465 time to fit residues: 116.5710 Evaluate side-chains 66 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.525 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0442 time to fit residues: 0.8023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 48 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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** J 628 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2571 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= 0.193 Angle : 0.513 5.209 6233 Z= 0.265 Chirality : 0.042 0.126 654 Planarity : 0.005 0.049 811 Dihedral : 6.177 83.850 618 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 2.57 % 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: 0.87 (0.37), residues: 201 sheet: 0.29 (0.82), residues: 47 loop : 0.62 (0.36), residues: 296 *********************** 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 76 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.554 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 70 average time/residue: 1.4706 time to fit residues: 106.4057 Evaluate side-chains 68 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.5073 time to fit residues: 2.3576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.0060 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 4594 Z= 0.235 Angle : 0.522 5.408 6233 Z= 0.269 Chirality : 0.042 0.127 654 Planarity : 0.004 0.041 811 Dihedral : 6.076 83.905 618 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 2.78 % 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: 0.85 (0.36), residues: 207 sheet: 0.27 (0.78), residues: 52 loop : 0.57 (0.37), residues: 285 *********************** 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 74 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.581 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 67 average time/residue: 1.4461 time to fit residues: 100.2760 Evaluate side-chains 64 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.0733 time to fit residues: 1.0507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8176 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 4594 Z= 0.234 Angle : 0.516 5.658 6233 Z= 0.265 Chirality : 0.042 0.126 654 Planarity : 0.004 0.042 811 Dihedral : 6.007 85.057 618 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 2.78 % 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: 0.75 (0.36), residues: 544 helix: 0.95 (0.36), residues: 207 sheet: 0.10 (0.77), residues: 46 loop : 0.38 (0.36), residues: 291 *********************** 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 72 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.534 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 65 average time/residue: 1.4385 time to fit residues: 96.7809 Evaluate side-chains 61 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.5850 time to fit residues: 2.5996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.0270 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- 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** J 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 4594 Z= 0.156 Angle : 0.466 5.187 6233 Z= 0.238 Chirality : 0.040 0.124 654 Planarity : 0.004 0.040 811 Dihedral : 5.777 87.110 618 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 1.71 % 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: 0.96 (0.36), residues: 544 helix: 1.19 (0.37), residues: 207 sheet: 0.12 (0.78), residues: 46 loop : 0.46 (0.37), residues: 291 *********************** 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 68 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.543 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 1.4551 time to fit residues: 97.8462 Evaluate side-chains 60 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0981 time to fit residues: 0.8554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 32 optimal weight: 0.0980 chunk 31 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.0060 chunk 33 optimal weight: 0.3980 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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: 0.8138 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 4594 Z= 0.159 Angle : 0.471 5.705 6233 Z= 0.237 Chirality : 0.041 0.124 654 Planarity : 0.004 0.039 811 Dihedral : 5.640 87.397 618 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 3.21 % 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: 0.98 (0.36), residues: 544 helix: 1.19 (0.37), residues: 207 sheet: 0.11 (0.78), residues: 46 loop : 0.50 (0.37), residues: 291 *********************** 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 73 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.504 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 68 average time/residue: 1.4381 time to fit residues: 101.1989 Evaluate side-chains 63 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.8170 time to fit residues: 2.4302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.0000 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.0020 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3341 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= 0.211 Angle : 0.502 5.974 6233 Z= 0.252 Chirality : 0.042 0.151 654 Planarity : 0.004 0.042 811 Dihedral : 5.739 86.563 618 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 2.36 % 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: 0.82 (0.36), residues: 544 helix: 1.03 (0.36), residues: 207 sheet: 0.00 (0.77), residues: 46 loop : 0.42 (0.37), residues: 291 *********************** 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 69 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.537 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 65 average time/residue: 1.4674 time to fit residues: 98.6524 Evaluate side-chains 64 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.695 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1775 time to fit residues: 1.3073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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** J 237 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4594 Z= 0.266 Angle : 0.558 8.402 6233 Z= 0.282 Chirality : 0.043 0.183 654 Planarity : 0.004 0.046 811 Dihedral : 5.864 85.894 618 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 2.14 % 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: 0.62 (0.35), residues: 544 helix: 0.91 (0.36), residues: 207 sheet: -0.09 (0.76), residues: 46 loop : 0.27 (0.36), residues: 291 *********************** 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 70 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.575 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 65 average time/residue: 1.5265 time to fit residues: 102.7833 Evaluate side-chains 64 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1585 time to fit residues: 1.1482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 0.0270 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 45 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 0.3438 ------------------------------------------------------------------------------- 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: 0.8153 moved from start: 0.3507 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= 0.183 Angle : 0.539 13.551 6233 Z= 0.267 Chirality : 0.042 0.166 654 Planarity : 0.004 0.040 811 Dihedral : 5.729 88.027 618 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 1.50 % 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: 0.70 (0.36), residues: 544 helix: 1.01 (0.37), residues: 207 sheet: -0.06 (0.76), residues: 46 loop : 0.29 (0.36), residues: 291 ********************** 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 64 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.529 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 63 average time/residue: 1.4959 time to fit residues: 97.4912 Evaluate side-chains 63 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0450 time to fit residues: 0.8154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.090456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073138 restraints weight = 7568.367| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.82 r_work: 0.2982 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 4594 Z= 0.263 Angle : 0.569 12.753 6233 Z= 0.281 Chirality : 0.043 0.203 654 Planarity : 0.004 0.044 811 Dihedral : 5.855 86.373 618 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 1.07 % 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: 0.50 (0.35), residues: 544 helix: 0.81 (0.36), residues: 207 sheet: -0.12 (0.75), residues: 46 loop : 0.19 (0.36), residues: 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.75 seconds wall clock time: 43 minutes 49.79 seconds (2629.79 seconds total)