Starting phenix.real_space_refine (version: dev) on Thu Feb 16 21:24:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhb_26511/02_2023/7uhb_26511.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhb_26511/02_2023/7uhb_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_26511/02_2023/7uhb_26511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhb_26511/02_2023/7uhb_26511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhb_26511/02_2023/7uhb_26511.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhb_26511/02_2023/7uhb_26511.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "K GLU 1": "OE1" <-> "OE2" Residue "K ASP 11": "OD1" <-> "OD2" Residue "K GLU 30": "OE1" <-> "OE2" Residue "K PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 1 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.90, per 1000 atoms: 0.89 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 - 3.50 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 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: 1.03 Conformation dependent library (CDL) restraints added in 366.3 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: 0.13 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: 0.53 Time building geometry restraints manager: 1.03 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 1.435 1.471 -0.036 1.10e-02 8.26e+03 1.09e+01 bond pdb=" C6 NAG A 1 " pdb=" O6 NAG A 1 " ideal model delta sigma weight residual 1.421 1.452 -0.031 1.00e-02 1.00e+04 9.46e+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=" 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: 93.68 - 101.71: 5 101.71 - 109.75: 344 109.75 - 117.78: 1283 117.78 - 125.82: 1321 125.82 - 133.85: 31 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: 1234 16.63 - 33.25: 51 33.25 - 49.88: 8 49.88 - 66.51: 1 66.51 - 83.14: 2 Dihedral angle restraints: 1296 sinusoidal: 504 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 1293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.275: 330 0.275 - 0.550: 2 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 2.520 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 2.520 ... (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 ========== 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 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. 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: 4.540 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: 14.440 Check model and map are aligned: 0.030 Process input model: 10.920 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:13.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5387 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 0.050 2193 Z= 0.716 Angle : 1.355 18.043 2984 Z= 0.942 Chirality : 0.122 1.375 334 Planarity : 0.005 0.017 384 Dihedral : 9.865 83.136 776 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 % 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 *********************** 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 : 0.316 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: 1.2812 time to fit residues: 72.0152 Evaluate side-chains 36 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.241 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3454 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 12 optimal weight: 0.0770 chunk 15 optimal weight: 0.0670 chunk 23 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN K 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 2193 Z= 0.327 Angle : 0.730 7.840 2984 Z= 0.379 Chirality : 0.047 0.164 334 Planarity : 0.006 0.043 384 Dihedral : 5.092 19.042 318 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.37 % Rotamer Outliers : 3.32 % 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: 0.11 (0.49), residues: 266 helix: -0.41 (0.55), residues: 92 sheet: 1.54 (0.74), residues: 46 loop : 0.04 (0.49), residues: 128 *********************** 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 51 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 46 average time/residue: 1.5141 time to fit residues: 70.8897 Evaluate side-chains 37 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.239 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.8785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 2193 Z= 0.330 Angle : 0.686 7.416 2984 Z= 0.366 Chirality : 0.047 0.194 334 Planarity : 0.005 0.045 384 Dihedral : 4.871 17.923 318 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 3.79 % 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 (0.49), residues: 266 helix: 0.41 (0.56), residues: 86 sheet: 1.35 (0.74), residues: 48 loop : 0.09 (0.51), residues: 132 *********************** 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 57 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 52 average time/residue: 1.2229 time to fit residues: 64.9534 Evaluate side-chains 42 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.238 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.1616 time to fit residues: 0.5056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.8088 moved from start: 0.9674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 2193 Z= 0.310 Angle : 0.577 6.591 2984 Z= 0.307 Chirality : 0.044 0.184 334 Planarity : 0.004 0.037 384 Dihedral : 4.629 16.347 318 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 4.74 % 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: 0.53 (0.49), residues: 266 helix: 0.62 (0.56), residues: 88 sheet: 1.17 (0.75), residues: 49 loop : -0.06 (0.50), residues: 129 *********************** 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 50 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 1.3255 time to fit residues: 60.8783 Evaluate side-chains 46 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.247 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0885 time to fit residues: 0.5618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.8134 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 : 0.004 0.032 2193 Z= 0.267 Angle : 0.534 5.818 2984 Z= 0.283 Chirality : 0.042 0.174 334 Planarity : 0.004 0.041 384 Dihedral : 4.423 16.432 318 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 5.21 % 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: 0.65 (0.49), residues: 266 helix: 0.81 (0.55), residues: 88 sheet: 0.98 (0.76), residues: 49 loop : 0.05 (0.51), residues: 129 *********************** 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 54 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 49 average time/residue: 1.3434 time to fit residues: 67.1025 Evaluate side-chains 46 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.227 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.7543 time to fit residues: 1.8549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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: 0.8124 moved from start: 1.0490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 2193 Z= 0.234 Angle : 0.505 5.366 2984 Z= 0.274 Chirality : 0.042 0.174 334 Planarity : 0.004 0.040 384 Dihedral : 4.356 15.762 318 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 2.84 % 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: 0.61 (0.49), residues: 266 helix: 0.82 (0.55), residues: 88 sheet: 0.71 (0.73), residues: 49 loop : 0.11 (0.52), residues: 129 *********************** 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 45 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 43 average time/residue: 1.3438 time to fit residues: 58.9622 Evaluate side-chains 45 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.8662 time to fit residues: 2.0897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 0.0000 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.0770 chunk 17 optimal weight: 0.0060 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 24 optimal weight: 0.0870 chunk 21 optimal weight: 0.0020 overall best weight: 0.0344 ------------------------------------------------------------------------------- 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: 0.8048 moved from start: 1.0522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 2193 Z= 0.116 Angle : 0.425 3.956 2984 Z= 0.237 Chirality : 0.039 0.123 334 Planarity : 0.003 0.037 384 Dihedral : 3.940 15.183 318 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 2.84 % 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: 0.83 (0.50), residues: 266 helix: 1.11 (0.57), residues: 88 sheet: 0.86 (0.76), residues: 49 loop : 0.15 (0.52), residues: 129 *********************** 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 47 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.285 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 1.4653 time to fit residues: 67.2348 Evaluate side-chains 44 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0245 time to fit residues: 0.4044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 14 optimal weight: 0.0170 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 17 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: K 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 1.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 2193 Z= 0.201 Angle : 0.476 4.777 2984 Z= 0.259 Chirality : 0.041 0.168 334 Planarity : 0.004 0.039 384 Dihedral : 4.105 15.512 318 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 4.27 % 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: 0.84 (0.50), residues: 266 helix: 1.10 (0.56), residues: 88 sheet: 0.72 (0.73), residues: 49 loop : 0.24 (0.53), residues: 129 *********************** 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 51 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.313 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 45 average time/residue: 1.3042 time to fit residues: 59.8978 Evaluate side-chains 45 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1456 time to fit residues: 0.6281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 21 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.8143 moved from start: 1.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 2193 Z= 0.276 Angle : 0.529 5.136 2984 Z= 0.284 Chirality : 0.043 0.182 334 Planarity : 0.004 0.038 384 Dihedral : 4.307 16.858 318 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.90 % 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: 0.74 (0.50), residues: 266 helix: 1.00 (0.56), residues: 88 sheet: 0.60 (0.72), residues: 49 loop : 0.23 (0.54), residues: 129 *********************** 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 45 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.242 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 1.3513 time to fit residues: 62.1475 Evaluate side-chains 44 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.253 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.3455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.0370 chunk 20 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 1 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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: 0.8133 moved from start: 1.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 2193 Z= 0.218 Angle : 0.503 5.255 2984 Z= 0.276 Chirality : 0.043 0.169 334 Planarity : 0.004 0.038 384 Dihedral : 4.276 15.526 318 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 2.84 % 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: 0.67 (0.50), residues: 266 helix: 0.94 (0.56), residues: 88 sheet: 0.56 (0.73), residues: 49 loop : 0.18 (0.53), residues: 129 ********************** 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 46 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.275 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 1.3222 time to fit residues: 58.1654 Evaluate side-chains 45 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.257 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1107 time to fit residues: 0.6115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.141179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113569 restraints weight = 2303.717| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.93 r_work: 0.3022 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 1.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2193 Z= 0.207 Angle : 0.503 5.391 2984 Z= 0.276 Chirality : 0.043 0.172 334 Planarity : 0.004 0.039 384 Dihedral : 4.199 15.248 318 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.42 % 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: 0.66 (0.50), residues: 266 helix: 0.98 (0.56), residues: 87 sheet: 0.54 (0.73), residues: 49 loop : 0.15 (0.53), residues: 130 =============================================================================== Job complete usr+sys time: 1724.01 seconds wall clock time: 31 minutes 20.07 seconds (1880.07 seconds total)