Starting phenix.real_space_refine on Mon Sep 23 12:17:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhb_26511/09_2024/7uhb_26511.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhb_26511/09_2024/7uhb_26511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhb_26511/09_2024/7uhb_26511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhb_26511/09_2024/7uhb_26511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhb_26511/09_2024/7uhb_26511.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhb_26511/09_2024/7uhb_26511.cif" } resolution = 3.0 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= -0.002 sd= 0.069 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 11 5.16 5 C 1373 2.51 5 N 358 2.21 5 O 399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2141 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1510 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 11, 'TRANS': 183} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 593 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.56, per 1000 atoms: 1.66 Number of scatterers: 2141 At special positions: 0 Unit cell: (57, 57, 77, 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 11 16.00 O 399 8.00 N 358 7.00 C 1373 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, 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=2.08 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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 BETA1-4 " NAG A 1 " - " NAG A 2 " BETA1-6 " NAG A 1 " - " FUC A 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN C 343 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 275.8 milliseconds 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 37.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.874A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.387A 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 502 through 505 Processing helix chain 'K' and resid 2 through 20 removed outlier: 3.780A pdb=" N VAL K 9 " --> pdb=" O GLN K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 23 No H-bonds generated for 'chain 'K' and resid 21 through 23' Processing helix chain 'K' and resid 26 through 49 removed outlier: 4.041A pdb=" N LEU K 44 " --> pdb=" O THR K 40 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE K 47 " --> pdb=" O MET K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 74 removed outlier: 3.624A pdb=" N GLU K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU K 72 " --> pdb=" O HIS K 68 " (cutoff:3.500A) 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 391 through 392 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 94 hydrogen bonds defined for protein. 243 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: 0.52 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 461 1.33 - 1.45: 585 1.45 - 1.58: 1133 1.58 - 1.71: 0 1.71 - 1.84: 14 Bond restraints: 2193 Sorted by residual: bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.471 -0.058 2.00e-02 2.50e+03 8.51e+00 bond pdb=" CA CYS C 336 " pdb=" C CYS C 336 " ideal model delta sigma weight residual 1.528 1.497 0.030 1.08e-02 8.57e+03 7.78e+00 bond pdb=" C5 FUC A 3 " pdb=" O5 FUC A 3 " ideal model delta sigma weight residual 1.423 1.476 -0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" CG ASP K 11 " pdb=" OD1 ASP K 11 " ideal model delta sigma weight residual 1.249 1.199 0.050 1.90e-02 2.77e+03 6.98e+00 bond pdb=" CA LYS K 48 " pdb=" C LYS K 48 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.35e-02 5.49e+03 6.70e+00 ... (remaining 2188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 2925 3.61 - 7.22: 49 7.22 - 10.83: 6 10.83 - 14.43: 2 14.43 - 18.04: 2 Bond angle restraints: 2984 Sorted by residual: angle pdb=" N ASN C 388 " pdb=" CA ASN C 388 " pdb=" C ASN C 388 " ideal model delta sigma weight residual 113.01 126.98 -13.97 1.20e+00 6.94e-01 1.36e+02 angle pdb=" C LEU C 387 " pdb=" CA LEU C 387 " pdb=" CB LEU C 387 " ideal model delta sigma weight residual 110.68 128.72 -18.04 1.70e+00 3.46e-01 1.13e+02 angle pdb=" N ASN C 388 " pdb=" CA ASN C 388 " pdb=" CB ASN C 388 " ideal model delta sigma weight residual 110.39 93.68 16.71 1.75e+00 3.27e-01 9.12e+01 angle pdb=" N LYS K 48 " pdb=" CA LYS K 48 " pdb=" C LYS K 48 " ideal model delta sigma weight residual 111.82 121.75 -9.93 1.16e+00 7.43e-01 7.33e+01 angle pdb=" N SER K 49 " pdb=" CA SER K 49 " pdb=" C SER K 49 " ideal model delta sigma weight residual 110.35 120.84 -10.49 1.38e+00 5.25e-01 5.77e+01 ... (remaining 2979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 1271 16.63 - 33.25: 52 33.25 - 49.88: 8 49.88 - 66.51: 1 66.51 - 83.14: 2 Dihedral angle restraints: 1334 sinusoidal: 542 harmonic: 792 Sorted by residual: dihedral pdb=" C LYS K 48 " pdb=" N LYS K 48 " pdb=" CA LYS K 48 " pdb=" CB LYS K 48 " ideal model delta harmonic sigma weight residual -122.60 -156.03 33.43 0 2.50e+00 1.60e-01 1.79e+02 dihedral pdb=" C LEU C 387 " pdb=" N LEU C 387 " pdb=" CA LEU C 387 " pdb=" CB LEU C 387 " ideal model delta harmonic sigma weight residual -122.60 -153.09 30.49 0 2.50e+00 1.60e-01 1.49e+02 dihedral pdb=" N LYS K 48 " pdb=" C LYS K 48 " pdb=" CA LYS K 48 " pdb=" CB LYS K 48 " ideal model delta harmonic sigma weight residual 122.80 152.94 -30.14 0 2.50e+00 1.60e-01 1.45e+02 ... (remaining 1331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.275: 331 0.275 - 0.550: 1 0.550 - 0.825: 0 0.825 - 1.100: 0 1.100 - 1.375: 2 Chirality restraints: 334 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.04e+01 chirality pdb=" CA LYS K 48 " pdb=" N LYS K 48 " pdb=" C LYS K 48 " pdb=" CB LYS K 48 " both_signs ideal model delta sigma weight residual False 2.51 1.14 1.38 2.00e-01 2.50e+01 4.73e+01 chirality pdb=" CA LEU C 387 " pdb=" N LEU C 387 " pdb=" C LEU C 387 " pdb=" CB LEU C 387 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.56e+01 ... (remaining 331 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 495 " 0.034 2.00e-02 2.50e+03 1.74e-02 6.07e+00 pdb=" CG TYR C 495 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR C 495 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR C 495 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR C 495 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 495 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 495 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 505 " 0.024 2.00e-02 2.50e+03 1.26e-02 3.16e+00 pdb=" CG TYR C 505 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR C 505 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR C 505 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR C 505 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C 505 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 505 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 505 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 505 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C TYR C 505 " 0.025 2.00e-02 2.50e+03 pdb=" O TYR C 505 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN C 506 " -0.008 2.00e-02 2.50e+03 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 1220 3.03 - 3.50: 1963 3.50 - 3.96: 3487 3.96 - 4.43: 4061 4.43 - 4.90: 6324 Nonbonded interactions: 17055 Sorted by model distance: nonbonded pdb=" N ASN C 334 " pdb=" OD1 ASN C 334 " model vdw 2.562 3.120 nonbonded pdb=" N ASN C 370 " pdb=" N SER C 371 " model vdw 2.580 2.560 nonbonded pdb=" N SER C 373 " pdb=" N PHE C 374 " model vdw 2.585 2.560 nonbonded pdb=" N LYS C 386 " pdb=" N LEU C 387 " model vdw 2.598 2.560 nonbonded pdb=" N ASP C 428 " pdb=" OD1 ASP C 428 " model vdw 2.599 3.120 ... (remaining 17050 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 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.430 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: 0.000 Load rotamer database and sin/cos tables:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5150 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 : 0.011 0.058 2193 Z= 0.738 Angle : 1.364 18.043 2984 Z= 0.924 Chirality : 0.123 1.375 334 Planarity : 0.005 0.017 384 Dihedral : 9.643 83.136 814 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.01 % Favored : 96.62 % Rotamer: Outliers : 1.42 % Allowed : 1.42 % Favored : 97.16 % Cbeta Deviations : 1.18 % 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: -0.52 (0.47), residues: 266 helix: -1.36 (0.48), residues: 93 sheet: 1.09 (0.73), residues: 49 loop : 0.06 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP C 353 HIS 0.003 0.001 HIS K 8 PHE 0.014 0.003 PHE C 392 TYR 0.034 0.005 TYR C 495 ARG 0.001 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 55 average time/residue: 1.2398 time to fit residues: 69.5843 Evaluate side-chains 36 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 12 optimal weight: 0.0770 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 2193 Z= 0.328 Angle : 0.803 8.993 2984 Z= 0.409 Chirality : 0.049 0.156 334 Planarity : 0.007 0.057 384 Dihedral : 5.123 18.016 356 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.84 % Allowed : 9.95 % Favored : 87.20 % 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: -0.33 (0.48), residues: 266 helix: -0.78 (0.53), residues: 92 sheet: 1.37 (0.74), residues: 46 loop : -0.25 (0.48), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 436 HIS 0.009 0.003 HIS K 18 PHE 0.015 0.003 PHE C 338 TYR 0.032 0.003 TYR C 495 ARG 0.008 0.001 ARG K 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: C 356 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7555 (ptmt) REVERT: C 391 CYS cc_start: 0.6491 (m) cc_final: 0.6263 (m) REVERT: C 399 SER cc_start: 0.8546 (p) cc_final: 0.8336 (m) REVERT: K 46 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7299 (tt) outliers start: 6 outliers final: 0 residues processed: 44 average time/residue: 1.4537 time to fit residues: 65.1759 Evaluate side-chains 39 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain K residue 46 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.0570 chunk 11 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 overall best weight: 0.2498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.7574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2193 Z= 0.215 Angle : 0.568 6.929 2984 Z= 0.304 Chirality : 0.042 0.141 334 Planarity : 0.005 0.033 384 Dihedral : 4.285 16.908 356 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.27 % Allowed : 13.74 % Favored : 81.99 % 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: 0.47 (0.49), residues: 266 helix: 0.35 (0.55), residues: 94 sheet: 1.27 (0.73), residues: 48 loop : 0.04 (0.50), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 353 HIS 0.003 0.001 HIS K 18 PHE 0.006 0.001 PHE C 515 TYR 0.021 0.002 TYR C 495 ARG 0.005 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: C 356 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8048 (tttt) REVERT: C 391 CYS cc_start: 0.6744 (m) cc_final: 0.6468 (m) REVERT: C 406 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: K 7 MET cc_start: 0.8053 (mmm) cc_final: 0.7629 (tpp) REVERT: K 63 ARG cc_start: 0.7410 (tpp-160) cc_final: 0.7142 (mtt-85) outliers start: 9 outliers final: 2 residues processed: 40 average time/residue: 1.4145 time to fit residues: 57.6773 Evaluate side-chains 36 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain K residue 46 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.9511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2193 Z= 0.286 Angle : 0.628 7.673 2984 Z= 0.328 Chirality : 0.045 0.193 334 Planarity : 0.005 0.055 384 Dihedral : 5.260 27.895 356 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.16 % Allowed : 12.80 % Favored : 81.04 % 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: 0.27 (0.49), residues: 266 helix: 0.05 (0.53), residues: 94 sheet: 1.26 (0.74), residues: 48 loop : -0.02 (0.50), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 436 HIS 0.006 0.002 HIS K 18 PHE 0.015 0.002 PHE C 486 TYR 0.027 0.002 TYR C 495 ARG 0.005 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7577 (mm-30) REVERT: C 498 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7292 (pt0) REVERT: K 7 MET cc_start: 0.8012 (mmm) cc_final: 0.7564 (tpp) REVERT: K 46 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7914 (tt) outliers start: 13 outliers final: 1 residues processed: 53 average time/residue: 1.3057 time to fit residues: 70.5194 Evaluate side-chains 45 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain K residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 1.0256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2193 Z= 0.330 Angle : 0.585 6.776 2984 Z= 0.312 Chirality : 0.044 0.161 334 Planarity : 0.005 0.056 384 Dihedral : 4.887 22.845 356 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.21 % Allowed : 17.06 % Favored : 77.73 % 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: 0.37 (0.49), residues: 266 helix: 0.74 (0.55), residues: 86 sheet: 0.97 (0.76), residues: 49 loop : -0.29 (0.49), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.004 0.001 HIS K 18 PHE 0.009 0.002 PHE C 377 TYR 0.019 0.002 TYR C 495 ARG 0.004 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7615 (mm-30) REVERT: C 472 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8101 (mm) outliers start: 11 outliers final: 5 residues processed: 50 average time/residue: 1.2343 time to fit residues: 62.9943 Evaluate side-chains 51 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 1.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2193 Z= 0.294 Angle : 0.569 6.428 2984 Z= 0.301 Chirality : 0.044 0.181 334 Planarity : 0.005 0.050 384 Dihedral : 4.916 23.085 356 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.27 % Allowed : 18.01 % Favored : 77.73 % 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: 0.46 (0.49), residues: 266 helix: 0.81 (0.55), residues: 88 sheet: 0.51 (0.70), residues: 49 loop : -0.01 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS K 18 PHE 0.005 0.001 PHE C 377 TYR 0.017 0.002 TYR C 495 ARG 0.003 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: C 472 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8194 (mm) outliers start: 9 outliers final: 5 residues processed: 47 average time/residue: 1.3394 time to fit residues: 64.2392 Evaluate side-chains 48 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN ** K 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 1.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 2193 Z= 0.401 Angle : 0.633 6.707 2984 Z= 0.337 Chirality : 0.047 0.173 334 Planarity : 0.005 0.055 384 Dihedral : 5.281 30.210 356 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.21 % Allowed : 17.54 % Favored : 77.25 % 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: 0.09 (0.48), residues: 266 helix: 0.57 (0.54), residues: 88 sheet: 0.30 (0.69), residues: 49 loop : -0.30 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 353 HIS 0.003 0.001 HIS K 18 PHE 0.007 0.002 PHE C 377 TYR 0.021 0.002 TYR C 495 ARG 0.004 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7671 (mm-30) REVERT: C 472 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8286 (mm) outliers start: 11 outliers final: 7 residues processed: 44 average time/residue: 1.3421 time to fit residues: 60.2503 Evaluate side-chains 48 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain K residue 45 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 0.0570 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 1.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2193 Z= 0.256 Angle : 0.540 6.018 2984 Z= 0.294 Chirality : 0.043 0.169 334 Planarity : 0.004 0.051 384 Dihedral : 5.016 25.988 356 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.32 % Allowed : 20.38 % Favored : 76.30 % 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: 0.23 (0.49), residues: 266 helix: 0.77 (0.55), residues: 88 sheet: 0.29 (0.70), residues: 49 loop : -0.23 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS K 18 PHE 0.005 0.001 PHE C 377 TYR 0.015 0.002 TYR C 495 ARG 0.003 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7606 (mm-30) REVERT: C 472 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8221 (mm) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 1.2863 time to fit residues: 55.1719 Evaluate side-chains 46 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.0170 chunk 6 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN K 12 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 1.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2193 Z= 0.206 Angle : 0.501 5.501 2984 Z= 0.276 Chirality : 0.042 0.147 334 Planarity : 0.004 0.051 384 Dihedral : 4.708 21.893 356 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.79 % Allowed : 19.91 % Favored : 76.30 % 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: 0.35 (0.49), residues: 266 helix: 0.94 (0.55), residues: 88 sheet: 0.20 (0.70), residues: 49 loop : -0.14 (0.52), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS K 18 PHE 0.005 0.001 PHE C 377 TYR 0.013 0.001 TYR C 495 ARG 0.002 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 406 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: C 472 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8211 (mm) outliers start: 8 outliers final: 3 residues processed: 42 average time/residue: 1.3106 time to fit residues: 56.1662 Evaluate side-chains 44 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 18 optimal weight: 0.0670 chunk 1 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 overall best weight: 0.1416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN K 12 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 1.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2193 Z= 0.132 Angle : 0.455 5.004 2984 Z= 0.253 Chirality : 0.041 0.131 334 Planarity : 0.004 0.049 384 Dihedral : 4.204 21.282 356 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.37 % Allowed : 21.80 % Favored : 75.83 % 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: 0.56 (0.50), residues: 266 helix: 1.19 (0.56), residues: 88 sheet: 0.26 (0.73), residues: 47 loop : -0.04 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.001 HIS K 18 PHE 0.005 0.001 PHE C 456 TYR 0.009 0.001 TYR C 505 ARG 0.005 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 399 SER cc_start: 0.8908 (p) cc_final: 0.8610 (m) REVERT: C 472 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8122 (mm) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 1.3380 time to fit residues: 57.3298 Evaluate side-chains 42 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.133189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.105565 restraints weight = 2374.909| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.91 r_work: 0.2989 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 1.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2193 Z= 0.297 Angle : 0.541 5.763 2984 Z= 0.292 Chirality : 0.044 0.166 334 Planarity : 0.004 0.051 384 Dihedral : 4.462 20.785 356 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.42 % Allowed : 22.27 % Favored : 76.30 % 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: 0.48 (0.50), residues: 266 helix: 1.06 (0.56), residues: 88 sheet: 0.19 (0.70), residues: 49 loop : -0.04 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS K 18 PHE 0.006 0.001 PHE C 377 TYR 0.016 0.002 TYR C 495 ARG 0.006 0.001 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1680.78 seconds wall clock time: 30 minutes 4.96 seconds (1804.96 seconds total)