Starting phenix.real_space_refine on Mon Mar 11 00:35:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrv_32736/03_2024/7wrv_32736_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrv_32736/03_2024/7wrv_32736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrv_32736/03_2024/7wrv_32736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrv_32736/03_2024/7wrv_32736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrv_32736/03_2024/7wrv_32736_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrv_32736/03_2024/7wrv_32736_neut.pdb" } resolution = 2.47 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= 0.060 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: 5 Type Number sf(0) Gaussians S 16 5.16 5 C 2087 2.51 5 N 543 2.21 5 O 621 1.98 5 H 3092 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "U GLU 107": "OE1" <-> "OE2" Residue "V GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6359 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 2966 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 186} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "U" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1814 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "V" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1579 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 3.21, per 1000 atoms: 0.50 Number of scatterers: 6359 At special positions: 0 Unit cell: (80.752, 60.976, 90.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 O 621 8.00 N 543 7.00 C 2087 6.00 H 3092 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 290 " - pdb=" SG CYS V 355 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 718.2 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 13.3% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.704A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.105A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.859A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.636A pdb=" N TYR U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'V' and resid 346 through 350 Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.560A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'U' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'U' and resid 10 through 12 removed outlier: 7.093A pdb=" N ILE U 34 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG U 50 " --> pdb=" O ILE U 34 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'U' and resid 10 through 12 removed outlier: 4.163A pdb=" N ILE U 112 " --> pdb=" O SER U 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 271 through 274 removed outlier: 5.298A pdb=" N THR V 336 " --> pdb=" O ALA V 292 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N GLN V 294 " --> pdb=" O SER V 334 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N SER V 334 " --> pdb=" O GLN V 294 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE V 296 " --> pdb=" O SER V 332 " (cutoff:3.500A) removed outlier: 11.711A pdb=" N SER V 332 " --> pdb=" O ILE V 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 277 through 279 removed outlier: 6.729A pdb=" N TRP V 302 " --> pdb=" O LEU V 314 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'V' and resid 277 through 279 removed outlier: 3.513A pdb=" N THR V 364 " --> pdb=" O GLN V 357 " (cutoff:3.500A) 118 hydrogen bonds defined for protein. 264 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3092 1.03 - 1.23: 0 1.23 - 1.42: 1483 1.42 - 1.62: 1849 1.62 - 1.81: 20 Bond restraints: 6444 Sorted by residual: bond pdb=" N GLU U 107 " pdb=" H GLU U 107 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.82e+00 bond pdb=" N GLU U 107 " pdb=" CA GLU U 107 " ideal model delta sigma weight residual 1.456 1.482 -0.027 1.44e-02 4.82e+03 3.44e+00 bond pdb=" N ASN C 331 " pdb=" CA ASN C 331 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ASN C 331 " pdb=" H ASN C 331 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" CB MET U 81 " pdb=" CG MET U 81 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 ... (remaining 6439 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.64: 109 106.64 - 113.50: 7207 113.50 - 120.35: 2215 120.35 - 127.20: 1986 127.20 - 134.05: 39 Bond angle restraints: 11556 Sorted by residual: angle pdb=" CB GLU U 107 " pdb=" CG GLU U 107 " pdb=" CD GLU U 107 " ideal model delta sigma weight residual 112.60 122.77 -10.17 1.70e+00 3.46e-01 3.58e+01 angle pdb=" CA GLU U 107 " pdb=" CB GLU U 107 " pdb=" CG GLU U 107 " ideal model delta sigma weight residual 114.10 108.35 5.75 2.00e+00 2.50e-01 8.25e+00 angle pdb=" CA GLU U 107 " pdb=" C GLU U 107 " pdb=" O GLU U 107 " ideal model delta sigma weight residual 121.49 118.50 2.99 1.16e+00 7.43e-01 6.64e+00 angle pdb=" CB MET U 81 " pdb=" CG MET U 81 " pdb=" SD MET U 81 " ideal model delta sigma weight residual 112.70 119.95 -7.25 3.00e+00 1.11e-01 5.84e+00 angle pdb=" N ILE C 410 " pdb=" CA ILE C 410 " pdb=" C ILE C 410 " ideal model delta sigma weight residual 106.21 108.78 -2.57 1.07e+00 8.73e-01 5.78e+00 ... (remaining 11551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.08: 2848 19.08 - 38.16: 187 38.16 - 57.24: 81 57.24 - 76.33: 5 76.33 - 95.41: 5 Dihedral angle restraints: 3126 sinusoidal: 1617 harmonic: 1509 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -161.72 75.72 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS U 22 " pdb=" SG CYS U 22 " pdb=" SG CYS U 96 " pdb=" CB CYS U 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.92 39.08 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB GLU U 107 " pdb=" CG GLU U 107 " pdb=" CD GLU U 107 " pdb=" OE1 GLU U 107 " ideal model delta sinusoidal sigma weight residual 0.00 95.41 -95.41 1 3.00e+01 1.11e-03 1.17e+01 ... (remaining 3123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 375 0.040 - 0.079: 71 0.079 - 0.119: 42 0.119 - 0.159: 8 0.159 - 0.198: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA GLU U 107 " pdb=" N GLU U 107 " pdb=" C GLU U 107 " pdb=" CB GLU U 107 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" CA ILE U 52 " pdb=" N ILE U 52 " pdb=" C ILE U 52 " pdb=" CB ILE U 52 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE V 342 " pdb=" N ILE V 342 " pdb=" C ILE V 342 " pdb=" CB ILE V 342 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 494 not shown) Planarity restraints: 991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU U 107 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" CD GLU U 107 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU U 107 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU U 107 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG V 285 " -0.135 9.50e-02 1.11e+02 4.55e-02 2.89e+00 pdb=" NE ARG V 285 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG V 285 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG V 285 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG V 285 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG V 285 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG V 285 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG V 285 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG V 285 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP U 106 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C TRP U 106 " -0.022 2.00e-02 2.50e+03 pdb=" O TRP U 106 " 0.008 2.00e-02 2.50e+03 pdb=" N GLU U 107 " 0.007 2.00e-02 2.50e+03 ... (remaining 988 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 453 2.21 - 2.81: 12881 2.81 - 3.40: 16507 3.40 - 4.00: 22758 4.00 - 4.60: 34243 Nonbonded interactions: 86842 Sorted by model distance: nonbonded pdb=" O GLY U 26 " pdb=" HH TYR U 32 " model vdw 1.611 1.850 nonbonded pdb=" OD1 ASP C 442 " pdb=" HH TYR C 451 " model vdw 1.644 1.850 nonbonded pdb=" HG2 GLU U 10 " pdb=" HE2 LYS U 12 " model vdw 1.682 2.440 nonbonded pdb="HH22 ARG C 454 " pdb=" O SER C 469 " model vdw 1.725 1.850 nonbonded pdb=" HG1 THR C 376 " pdb=" O ALA C 435 " model vdw 1.737 1.850 ... (remaining 86837 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: 6.080 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: 0.110 Extract box with map and model: 23.460 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 24.780 Find NCS groups from input model: 0.120 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3352 Z= 0.161 Angle : 0.601 10.169 4564 Z= 0.338 Chirality : 0.044 0.198 497 Planarity : 0.004 0.061 588 Dihedral : 14.423 95.407 1165 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.58 % Allowed : 10.14 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.27 (0.41), residues: 421 helix: -2.90 (1.06), residues: 21 sheet: 1.01 (0.43), residues: 164 loop : -0.07 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 299 HIS 0.001 0.000 HIS C 519 PHE 0.007 0.001 PHE C 490 TYR 0.021 0.001 TYR V 316 ARG 0.014 0.001 ARG V 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4841 (tttt) cc_final: 0.3259 (ttpt) REVERT: V 349 ASP cc_start: 0.6610 (m-30) cc_final: 0.6350 (m-30) outliers start: 2 outliers final: 0 residues processed: 74 average time/residue: 2.5008 time to fit residues: 190.1166 Evaluate side-chains 47 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 ASN C 505 HIS U 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3352 Z= 0.195 Angle : 0.534 4.330 4564 Z= 0.288 Chirality : 0.045 0.152 497 Planarity : 0.004 0.024 588 Dihedral : 4.510 16.237 467 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.32 % Allowed : 14.20 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.14 (0.41), residues: 421 helix: -3.17 (0.94), residues: 21 sheet: 0.95 (0.42), residues: 164 loop : -0.17 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 47 HIS 0.001 0.001 HIS C 519 PHE 0.010 0.001 PHE C 490 TYR 0.012 0.001 TYR V 316 ARG 0.003 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.5012 (OUTLIER) cc_final: 0.3184 (ttpt) REVERT: U 48 MET cc_start: 0.6955 (mtp) cc_final: 0.6727 (mtp) REVERT: V 349 ASP cc_start: 0.6889 (m-30) cc_final: 0.6670 (m-30) outliers start: 8 outliers final: 2 residues processed: 60 average time/residue: 2.6841 time to fit residues: 165.5755 Evaluate side-chains 52 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3352 Z= 0.200 Angle : 0.528 3.969 4564 Z= 0.284 Chirality : 0.045 0.138 497 Planarity : 0.004 0.050 588 Dihedral : 4.649 17.440 467 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.74 % Allowed : 18.26 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.07 (0.41), residues: 421 helix: -3.09 (1.01), residues: 21 sheet: 0.86 (0.42), residues: 159 loop : -0.34 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 47 HIS 0.002 0.001 HIS C 519 PHE 0.012 0.001 PHE C 377 TYR 0.016 0.002 TYR U 32 ARG 0.006 0.001 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4948 (tttt) cc_final: 0.2912 (ttmt) REVERT: U 48 MET cc_start: 0.7199 (mtp) cc_final: 0.6871 (mtp) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 2.3087 time to fit residues: 131.5918 Evaluate side-chains 50 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3352 Z= 0.189 Angle : 0.518 4.127 4564 Z= 0.277 Chirality : 0.045 0.138 497 Planarity : 0.004 0.029 588 Dihedral : 4.644 17.608 467 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.74 % Allowed : 18.84 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.25 (0.41), residues: 421 helix: -3.66 (1.20), residues: 14 sheet: 0.77 (0.42), residues: 159 loop : -0.58 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 47 HIS 0.001 0.001 HIS C 505 PHE 0.010 0.001 PHE C 490 TYR 0.014 0.002 TYR V 316 ARG 0.004 0.000 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4955 (tttt) cc_final: 0.2926 (ttmt) REVERT: U 48 MET cc_start: 0.7223 (mtp) cc_final: 0.6908 (mtp) REVERT: U 112 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7885 (mp) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 2.1482 time to fit residues: 122.6653 Evaluate side-chains 51 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.0030 chunk 7 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 3 GLN U 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3352 Z= 0.165 Angle : 0.498 4.077 4564 Z= 0.266 Chirality : 0.045 0.134 497 Planarity : 0.004 0.024 588 Dihedral : 4.492 16.956 467 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.45 % Allowed : 19.71 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.23 (0.41), residues: 421 helix: -3.60 (1.25), residues: 14 sheet: 0.80 (0.42), residues: 159 loop : -0.57 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 47 HIS 0.001 0.001 HIS C 505 PHE 0.009 0.001 PHE C 490 TYR 0.014 0.001 TYR U 32 ARG 0.004 0.000 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4922 (tttt) cc_final: 0.2922 (ttmt) REVERT: U 48 MET cc_start: 0.7246 (mtp) cc_final: 0.6922 (mtp) outliers start: 5 outliers final: 5 residues processed: 51 average time/residue: 2.0373 time to fit residues: 108.4642 Evaluate side-chains 50 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3352 Z= 0.192 Angle : 0.507 4.163 4564 Z= 0.272 Chirality : 0.045 0.136 497 Planarity : 0.004 0.024 588 Dihedral : 4.566 17.086 467 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.90 % Allowed : 19.13 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.26 (0.41), residues: 421 helix: -3.52 (1.29), residues: 14 sheet: 0.82 (0.42), residues: 159 loop : -0.63 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 47 HIS 0.001 0.001 HIS C 505 PHE 0.010 0.001 PHE V 340 TYR 0.014 0.002 TYR U 32 ARG 0.004 0.000 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4923 (tttt) cc_final: 0.3005 (ttmt) REVERT: U 48 MET cc_start: 0.7288 (mtp) cc_final: 0.6941 (mtp) REVERT: U 112 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7816 (mp) outliers start: 10 outliers final: 5 residues processed: 56 average time/residue: 2.3282 time to fit residues: 134.9484 Evaluate side-chains 51 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3352 Z= 0.189 Angle : 0.510 4.209 4564 Z= 0.272 Chirality : 0.045 0.135 497 Planarity : 0.004 0.029 588 Dihedral : 4.563 16.963 467 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.32 % Allowed : 18.84 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.37 (0.41), residues: 421 helix: -3.53 (1.31), residues: 14 sheet: 0.73 (0.42), residues: 157 loop : -0.68 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 47 HIS 0.001 0.001 HIS C 519 PHE 0.010 0.001 PHE V 340 TYR 0.012 0.001 TYR U 32 ARG 0.003 0.000 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4918 (tttt) cc_final: 0.3007 (ttmt) REVERT: U 48 MET cc_start: 0.7294 (mtp) cc_final: 0.6937 (mtp) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 2.1191 time to fit residues: 112.1833 Evaluate side-chains 51 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3352 Z= 0.203 Angle : 0.516 4.247 4564 Z= 0.277 Chirality : 0.045 0.136 497 Planarity : 0.004 0.024 588 Dihedral : 4.630 17.071 467 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.32 % Allowed : 19.13 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.43 (0.41), residues: 421 helix: -3.60 (1.26), residues: 14 sheet: 0.68 (0.42), residues: 157 loop : -0.72 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 47 HIS 0.002 0.001 HIS C 519 PHE 0.010 0.001 PHE V 340 TYR 0.013 0.002 TYR U 32 ARG 0.003 0.000 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4925 (tttt) cc_final: 0.3123 (ttmt) REVERT: C 408 ARG cc_start: 0.7418 (ttp80) cc_final: 0.7130 (ptt90) REVERT: U 48 MET cc_start: 0.7343 (mtp) cc_final: 0.7057 (mtp) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 2.0979 time to fit residues: 109.2961 Evaluate side-chains 48 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3352 Z= 0.228 Angle : 0.534 4.348 4564 Z= 0.288 Chirality : 0.045 0.136 497 Planarity : 0.004 0.027 588 Dihedral : 4.738 17.526 467 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.03 % Allowed : 19.42 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 (0.40), residues: 421 helix: -3.53 (1.28), residues: 14 sheet: 0.75 (0.44), residues: 146 loop : -0.80 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP U 47 HIS 0.002 0.001 HIS C 505 PHE 0.011 0.001 PHE V 340 TYR 0.014 0.002 TYR V 316 ARG 0.002 0.001 ARG U 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4939 (tttt) cc_final: 0.3161 (ttmt) REVERT: U 48 MET cc_start: 0.7358 (mtp) cc_final: 0.6980 (mtp) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 1.9884 time to fit residues: 101.1292 Evaluate side-chains 47 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3352 Z= 0.207 Angle : 0.526 4.344 4564 Z= 0.282 Chirality : 0.045 0.135 497 Planarity : 0.004 0.024 588 Dihedral : 4.674 17.466 467 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.74 % Allowed : 19.71 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.57 (0.41), residues: 421 helix: -3.56 (1.03), residues: 20 sheet: 0.79 (0.44), residues: 146 loop : -0.83 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 47 HIS 0.002 0.001 HIS C 519 PHE 0.010 0.001 PHE V 340 TYR 0.012 0.002 TYR V 316 ARG 0.003 0.000 ARG U 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 332 is missing expected H atoms. Skipping. Residue LYS 356 is missing expected H atoms. Skipping. Residue THR 415 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue SER 459 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 523 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.4911 (tttt) cc_final: 0.3009 (ttmt) REVERT: C 408 ARG cc_start: 0.7470 (ttp80) cc_final: 0.7216 (ptt90) REVERT: U 48 MET cc_start: 0.7356 (mtp) cc_final: 0.6981 (mtp) outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 2.1509 time to fit residues: 102.4204 Evaluate side-chains 46 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain V residue 297 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.171333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.156524 restraints weight = 14346.331| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 1.79 r_work: 0.4012 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3352 Z= 0.171 Angle : 0.505 4.225 4564 Z= 0.269 Chirality : 0.045 0.133 497 Planarity : 0.004 0.024 588 Dihedral : 4.492 16.805 467 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.74 % Allowed : 19.42 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.54 (0.40), residues: 421 helix: -3.49 (1.07), residues: 20 sheet: 0.84 (0.44), residues: 146 loop : -0.83 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 47 HIS 0.001 0.001 HIS C 505 PHE 0.009 0.001 PHE V 340 TYR 0.011 0.001 TYR U 32 ARG 0.003 0.000 ARG U 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4244.14 seconds wall clock time: 75 minutes 27.52 seconds (4527.52 seconds total)