Starting phenix.real_space_refine on Thu Nov 14 00:42:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgt_50424/11_2024/9fgt_50424.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgt_50424/11_2024/9fgt_50424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgt_50424/11_2024/9fgt_50424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgt_50424/11_2024/9fgt_50424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgt_50424/11_2024/9fgt_50424.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgt_50424/11_2024/9fgt_50424.cif" } resolution = 3.8 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= -0.006 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1863 2.51 5 N 496 2.21 5 O 552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2921 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 2 Chain: "E" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1627 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.49, per 1000 atoms: 1.19 Number of scatterers: 2921 At special positions: 0 Unit cell: (78.232, 65.786, 79.121, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 552 8.00 N 496 7.00 C 1863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 377.4 milliseconds 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 676 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 9 sheets defined 8.0% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.523A pdb=" N ASN C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.211A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.589A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.884A pdb=" N GLY C 482 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.586A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 396 through 397 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.761A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 18 " --> pdb=" O MET E 82 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.921A pdb=" N ALA E 96 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR E 33 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AA8, first strand: chain 'E' and resid 179 through 182 removed outlier: 6.668A pdb=" N TRP E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 221 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 172 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR E 231 " --> pdb=" O GLN E 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 179 through 182 removed outlier: 6.668A pdb=" N TRP E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 221 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 172 " --> pdb=" O VAL E 219 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.76 Time building geometry restraints manager: 0.79 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: 925 1.34 - 1.46: 657 1.46 - 1.57: 1399 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 2993 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.446 -0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" CA VAL C 395 " pdb=" C VAL C 395 " ideal model delta sigma weight residual 1.525 1.502 0.023 2.10e-02 2.27e+03 1.21e+00 bond pdb=" C SER E 100 " pdb=" O SER E 100 " ideal model delta sigma weight residual 1.235 1.222 0.013 1.26e-02 6.30e+03 1.12e+00 bond pdb=" CB TRP E 47 " pdb=" CG TRP E 47 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.04e+00 ... (remaining 2988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 3878 1.51 - 3.03: 150 3.03 - 4.54: 21 4.54 - 6.05: 8 6.05 - 7.56: 1 Bond angle restraints: 4058 Sorted by residual: angle pdb=" C ASN C 343 " pdb=" CA ASN C 343 " pdb=" CB ASN C 343 " ideal model delta sigma weight residual 109.80 115.12 -5.32 1.70e+00 3.46e-01 9.80e+00 angle pdb=" C PRO C 479 " pdb=" N CYS C 480 " pdb=" CA CYS C 480 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.18e+00 angle pdb=" C LEU E 99 " pdb=" N SER E 100 " pdb=" CA SER E 100 " ideal model delta sigma weight residual 121.54 126.93 -5.39 1.91e+00 2.74e-01 7.98e+00 angle pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " pdb=" C5 NAG C1301 " ideal model delta sigma weight residual 113.21 120.77 -7.56 3.00e+00 1.11e-01 6.36e+00 angle pdb=" CA ASP C 428 " pdb=" CB ASP C 428 " pdb=" CG ASP C 428 " ideal model delta sigma weight residual 112.60 114.61 -2.01 1.00e+00 1.00e+00 4.05e+00 ... (remaining 4053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 1640 22.35 - 44.69: 96 44.69 - 67.04: 21 67.04 - 89.39: 0 89.39 - 111.73: 3 Dihedral angle restraints: 1760 sinusoidal: 691 harmonic: 1069 Sorted by residual: dihedral pdb=" CB CYS E 156 " pdb=" SG CYS E 156 " pdb=" SG CYS E 222 " pdb=" CB CYS E 222 " ideal model delta sinusoidal sigma weight residual 93.00 145.53 -52.53 1 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" C1 NAG C1301 " pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " pdb=" C4 NAG C1301 " ideal model delta sinusoidal sigma weight residual -64.11 47.62 -111.73 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C1 NAG C1301 " pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " pdb=" C6 NAG C1301 " ideal model delta sinusoidal sigma weight residual 171.16 -78.54 -110.30 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 1757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 319 0.047 - 0.094: 84 0.094 - 0.141: 29 0.141 - 0.188: 1 0.188 - 0.236: 2 Chirality restraints: 435 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CG LEU E 167 " pdb=" CB LEU E 167 " pdb=" CD1 LEU E 167 " pdb=" CD2 LEU E 167 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 432 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 13 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO E 14 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 225 " -0.012 2.00e-02 2.50e+03 1.31e-02 3.44e+00 pdb=" CG TYR E 225 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR E 225 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR E 225 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR E 225 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR E 225 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 225 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 225 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 453 " 0.016 2.00e-02 2.50e+03 1.13e-02 2.54e+00 pdb=" CG TYR C 453 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR C 453 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 453 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 453 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 453 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 453 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 453 " 0.002 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 44 2.66 - 3.22: 2668 3.22 - 3.78: 3965 3.78 - 4.34: 5381 4.34 - 4.90: 9059 Nonbonded interactions: 21117 Sorted by model distance: nonbonded pdb=" OH TYR C 421 " pdb=" O PRO E 53 " model vdw 2.094 3.040 nonbonded pdb=" O GLY E 142 " pdb=" OG1 THR E 236 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR C 376 " pdb=" O ALA C 435 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR C 473 " pdb=" O ALA E 31 " model vdw 2.303 3.040 nonbonded pdb=" NH1 ARG E 188 " pdb=" O PHE E 196 " model vdw 2.315 3.120 ... (remaining 21112 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.570 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 2993 Z= 0.339 Angle : 0.703 7.564 4058 Z= 0.370 Chirality : 0.049 0.236 435 Planarity : 0.005 0.050 521 Dihedral : 14.859 111.732 1072 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.43), residues: 361 helix: -3.41 (1.05), residues: 13 sheet: -0.18 (0.51), residues: 117 loop : -1.41 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.017 0.002 PHE E 205 TYR 0.029 0.002 TYR E 225 ARG 0.004 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.340 Fit side-chains REVERT: C 458 LYS cc_start: 0.8502 (mttt) cc_final: 0.8291 (mttp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1190 time to fit residues: 8.4250 Evaluate side-chains 49 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 32 optimal weight: 0.0470 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2993 Z= 0.212 Angle : 0.685 12.597 4058 Z= 0.342 Chirality : 0.047 0.143 435 Planarity : 0.005 0.052 521 Dihedral : 9.091 73.607 436 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.93 % Allowed : 10.29 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.43), residues: 361 helix: -3.21 (1.17), residues: 13 sheet: 0.03 (0.53), residues: 110 loop : -1.36 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.001 0.001 HIS C 505 PHE 0.008 0.001 PHE E 205 TYR 0.018 0.001 TYR E 225 ARG 0.003 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.321 Fit side-chains REVERT: C 406 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7684 (mt-10) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.1309 time to fit residues: 9.7537 Evaluate side-chains 59 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2993 Z= 0.223 Angle : 0.618 7.482 4058 Z= 0.314 Chirality : 0.046 0.181 435 Planarity : 0.004 0.051 521 Dihedral : 6.940 59.340 436 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.57 % Allowed : 13.18 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.43), residues: 361 helix: -3.29 (1.13), residues: 13 sheet: -0.03 (0.54), residues: 110 loop : -1.46 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 169 HIS 0.001 0.001 HIS C 505 PHE 0.021 0.001 PHE C 486 TYR 0.014 0.001 TYR E 225 ARG 0.003 0.000 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.306 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 56 average time/residue: 0.1070 time to fit residues: 7.8466 Evaluate side-chains 57 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2993 Z= 0.156 Angle : 0.568 7.132 4058 Z= 0.289 Chirality : 0.044 0.138 435 Planarity : 0.004 0.051 521 Dihedral : 6.294 59.493 436 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.57 % Allowed : 14.15 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.43), residues: 361 helix: -2.87 (1.35), residues: 13 sheet: 0.12 (0.55), residues: 108 loop : -1.45 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.000 0.000 HIS C 505 PHE 0.006 0.001 PHE E 205 TYR 0.014 0.001 TYR E 225 ARG 0.002 0.000 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.321 Fit side-chains REVERT: C 473 TYR cc_start: 0.8231 (t80) cc_final: 0.7989 (t80) REVERT: E 83 ASN cc_start: 0.7961 (m110) cc_final: 0.7571 (m-40) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.1122 time to fit residues: 9.2197 Evaluate side-chains 60 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 14 optimal weight: 0.0870 chunk 29 optimal weight: 0.0060 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.2752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2993 Z= 0.161 Angle : 0.573 7.128 4058 Z= 0.291 Chirality : 0.044 0.139 435 Planarity : 0.004 0.051 521 Dihedral : 5.752 55.825 436 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.25 % Allowed : 15.11 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.43), residues: 361 helix: -2.58 (1.54), residues: 13 sheet: 0.15 (0.55), residues: 107 loop : -1.48 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 108 HIS 0.000 0.000 HIS C 505 PHE 0.028 0.001 PHE E 205 TYR 0.015 0.001 TYR E 225 ARG 0.002 0.000 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.300 Fit side-chains REVERT: C 473 TYR cc_start: 0.8191 (t80) cc_final: 0.7978 (t80) REVERT: E 83 ASN cc_start: 0.7970 (m110) cc_final: 0.7562 (m-40) outliers start: 7 outliers final: 7 residues processed: 57 average time/residue: 0.1108 time to fit residues: 8.1927 Evaluate side-chains 58 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.0070 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2993 Z= 0.192 Angle : 0.583 7.459 4058 Z= 0.294 Chirality : 0.044 0.139 435 Planarity : 0.004 0.051 521 Dihedral : 5.555 54.315 436 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.22 % Allowed : 15.43 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.43), residues: 361 helix: -2.57 (1.57), residues: 13 sheet: 0.06 (0.55), residues: 107 loop : -1.54 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 108 HIS 0.001 0.001 HIS C 505 PHE 0.013 0.001 PHE E 205 TYR 0.013 0.001 TYR E 225 ARG 0.001 0.000 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.291 Fit side-chains REVERT: C 473 TYR cc_start: 0.8192 (t80) cc_final: 0.7985 (t80) REVERT: E 83 ASN cc_start: 0.7980 (m110) cc_final: 0.7584 (m-40) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.1160 time to fit residues: 8.4457 Evaluate side-chains 57 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.4980 chunk 29 optimal weight: 0.0370 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2993 Z= 0.222 Angle : 0.601 7.366 4058 Z= 0.304 Chirality : 0.045 0.141 435 Planarity : 0.004 0.052 521 Dihedral : 5.570 52.905 436 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.22 % Allowed : 16.72 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.43), residues: 361 helix: -2.86 (1.37), residues: 13 sheet: 0.00 (0.54), residues: 108 loop : -1.58 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.001 0.001 HIS C 505 PHE 0.031 0.002 PHE C 486 TYR 0.013 0.001 TYR E 225 ARG 0.002 0.000 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.335 Fit side-chains REVERT: E 82 MET cc_start: 0.8629 (mtm) cc_final: 0.8399 (mtt) REVERT: E 83 ASN cc_start: 0.7999 (m110) cc_final: 0.7594 (m-40) outliers start: 10 outliers final: 9 residues processed: 56 average time/residue: 0.1267 time to fit residues: 8.9902 Evaluate side-chains 54 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.0020 chunk 19 optimal weight: 0.1980 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 overall best weight: 0.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2993 Z= 0.161 Angle : 0.576 7.254 4058 Z= 0.290 Chirality : 0.044 0.139 435 Planarity : 0.004 0.053 521 Dihedral : 5.342 54.702 436 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.54 % Allowed : 17.68 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.43), residues: 361 helix: -2.73 (1.47), residues: 13 sheet: 0.22 (0.54), residues: 107 loop : -1.59 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.001 0.000 HIS C 505 PHE 0.029 0.001 PHE C 486 TYR 0.015 0.001 TYR E 225 ARG 0.001 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.327 Fit side-chains REVERT: E 83 ASN cc_start: 0.7991 (m110) cc_final: 0.7594 (m-40) outliers start: 11 outliers final: 8 residues processed: 56 average time/residue: 0.1274 time to fit residues: 9.1228 Evaluate side-chains 54 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.0020 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.0170 chunk 21 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.3426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 0.035 2993 Z= 0.184 Angle : 0.600 7.256 4058 Z= 0.296 Chirality : 0.044 0.135 435 Planarity : 0.004 0.053 521 Dihedral : 5.298 52.852 436 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.54 % Allowed : 18.01 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.43), residues: 361 helix: -2.73 (1.51), residues: 13 sheet: 0.23 (0.55), residues: 107 loop : -1.58 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.001 0.000 HIS C 505 PHE 0.032 0.001 PHE C 486 TYR 0.013 0.001 TYR E 225 ARG 0.002 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.329 Fit side-chains REVERT: E 83 ASN cc_start: 0.7906 (m110) cc_final: 0.7587 (m-40) outliers start: 11 outliers final: 9 residues processed: 55 average time/residue: 0.1097 time to fit residues: 7.9222 Evaluate side-chains 56 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 0.0270 chunk 29 optimal weight: 0.7980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2993 Z= 0.205 Angle : 0.614 7.461 4058 Z= 0.307 Chirality : 0.045 0.139 435 Planarity : 0.004 0.053 521 Dihedral : 5.357 52.596 436 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.57 % Allowed : 19.61 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.43), residues: 361 helix: -2.67 (1.55), residues: 13 sheet: 0.20 (0.55), residues: 107 loop : -1.60 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.001 0.001 HIS C 505 PHE 0.027 0.001 PHE C 486 TYR 0.013 0.001 TYR E 225 ARG 0.002 0.000 ARG C 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.370 Fit side-chains REVERT: E 83 ASN cc_start: 0.7886 (m110) cc_final: 0.7587 (m-40) outliers start: 8 outliers final: 8 residues processed: 54 average time/residue: 0.1112 time to fit residues: 8.0810 Evaluate side-chains 56 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130429 restraints weight = 5064.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133347 restraints weight = 3054.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.135225 restraints weight = 2123.181| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2993 Z= 0.260 Angle : 0.664 10.947 4058 Z= 0.326 Chirality : 0.045 0.134 435 Planarity : 0.004 0.053 521 Dihedral : 5.517 50.460 436 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.89 % Allowed : 19.29 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.43), residues: 361 helix: -2.94 (1.43), residues: 13 sheet: -0.01 (0.55), residues: 109 loop : -1.58 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 169 HIS 0.001 0.001 HIS C 505 PHE 0.027 0.001 PHE C 486 TYR 0.015 0.001 TYR E 225 ARG 0.002 0.000 ARG E 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1305.42 seconds wall clock time: 24 minutes 19.06 seconds (1459.06 seconds total)