Starting phenix.real_space_refine on Sun Mar 10 16:36:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcq_38251/03_2024/8xcq_38251_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcq_38251/03_2024/8xcq_38251.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcq_38251/03_2024/8xcq_38251_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcq_38251/03_2024/8xcq_38251_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcq_38251/03_2024/8xcq_38251_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcq_38251/03_2024/8xcq_38251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcq_38251/03_2024/8xcq_38251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcq_38251/03_2024/8xcq_38251_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcq_38251/03_2024/8xcq_38251_updated.pdb" } resolution = 2.6 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2099 2.51 5 N 560 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3312 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3255 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 57 Unusual residues: {'NAP': 1} Classifications: {'peptide': 2, 'undetermined': 1, 'water': 6} Link IDs: {'TRANS': 1, None: 7} Not linked: pdbres="NAP A 500 " pdbres="GGL A 501 " Not linked: pdbres="GGL A 502 " pdbres="HOH A 601 " Not linked: pdbres="HOH A 601 " pdbres="HOH A 602 " Not linked: pdbres="HOH A 602 " pdbres="HOH A 603 " Not linked: pdbres="HOH A 603 " pdbres="HOH A 604 " ... (remaining 2 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 2.42, per 1000 atoms: 0.73 Number of scatterers: 3312 At special positions: 0 Unit cell: (71.44, 69.936, 70.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 636 8.00 N 560 7.00 C 2099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 796.2 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 4 sheets defined 49.5% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.998A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.504A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.843A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 286 removed outlier: 4.466A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 340 through 360 removed outlier: 4.714A pdb=" N ALA A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.464A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 removed outlier: 6.987A pdb=" N GLY A 106 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N HIS A 75 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE A 108 " --> pdb=" O HIS A 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.152A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.609A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 161 hydrogen bonds defined for protein. 468 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: 0.91 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1066 1.34 - 1.46: 603 1.46 - 1.57: 1681 1.57 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3379 Sorted by residual: bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.566 0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" C4A NAP A 500 " pdb=" N3A NAP A 500 " ideal model delta sigma weight residual 1.332 1.438 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C6A NAP A 500 " pdb=" N6A NAP A 500 " ideal model delta sigma weight residual 1.335 1.433 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C8A NAP A 500 " pdb=" N7A NAP A 500 " ideal model delta sigma weight residual 1.301 1.399 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C8A NAP A 500 " pdb=" N9A NAP A 500 " ideal model delta sigma weight residual 1.371 1.462 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 3374 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.49: 100 106.49 - 113.39: 1853 113.39 - 120.30: 1234 120.30 - 127.20: 1352 127.20 - 134.10: 49 Bond angle restraints: 4588 Sorted by residual: angle pdb=" N ARG A 187 " pdb=" CA ARG A 187 " pdb=" C ARG A 187 " ideal model delta sigma weight residual 112.89 118.13 -5.24 1.24e+00 6.50e-01 1.79e+01 angle pdb=" O1A NAP A 500 " pdb=" PA NAP A 500 " pdb=" O2A NAP A 500 " ideal model delta sigma weight residual 121.77 109.72 12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O1N NAP A 500 " pdb=" PN NAP A 500 " pdb=" O2N NAP A 500 " ideal model delta sigma weight residual 122.51 110.57 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C PHE A 273 " pdb=" N PRO A 274 " pdb=" CA PRO A 274 " ideal model delta sigma weight residual 119.90 123.89 -3.99 1.02e+00 9.61e-01 1.53e+01 angle pdb=" N ARG A 16 " pdb=" CA ARG A 16 " pdb=" C ARG A 16 " ideal model delta sigma weight residual 111.28 107.26 4.02 1.09e+00 8.42e-01 1.36e+01 ... (remaining 4583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 1765 16.85 - 33.70: 169 33.70 - 50.55: 69 50.55 - 67.40: 25 67.40 - 84.25: 11 Dihedral angle restraints: 2039 sinusoidal: 846 harmonic: 1193 Sorted by residual: dihedral pdb=" CA ASP A 48 " pdb=" CB ASP A 48 " pdb=" CG ASP A 48 " pdb=" OD1 ASP A 48 " ideal model delta sinusoidal sigma weight residual -30.00 -86.89 56.89 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 163.88 16.12 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CG ARG A 187 " pdb=" CD ARG A 187 " pdb=" NE ARG A 187 " pdb=" CZ ARG A 187 " ideal model delta sinusoidal sigma weight residual -180.00 -136.67 -43.33 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 2036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 396 0.059 - 0.118: 87 0.118 - 0.177: 14 0.177 - 0.236: 1 0.236 - 0.294: 1 Chirality restraints: 499 Sorted by residual: chirality pdb=" C2B NAP A 500 " pdb=" C1B NAP A 500 " pdb=" C3B NAP A 500 " pdb=" O2B NAP A 500 " both_signs ideal model delta sigma weight residual False -2.75 -2.46 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ARG A 187 " pdb=" N ARG A 187 " pdb=" C ARG A 187 " pdb=" CB ARG A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CA ASP A 98 " pdb=" N ASP A 98 " pdb=" C ASP A 98 " pdb=" CB ASP A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.51e-01 ... (remaining 496 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 399 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.36e+00 pdb=" C ALA A 399 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA A 399 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 400 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 18 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C ALA A 18 " -0.036 2.00e-02 2.50e+03 pdb=" O ALA A 18 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 19 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO A 150 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.025 5.00e-02 4.00e+02 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 1400 2.93 - 3.42: 3329 3.42 - 3.91: 5794 3.91 - 4.41: 6772 4.41 - 4.90: 10822 Nonbonded interactions: 28117 Sorted by model distance: nonbonded pdb=" O1N NAP A 500 " pdb=" O2A NAP A 500 " model vdw 2.433 3.040 nonbonded pdb=" NH2 ARG A 58 " pdb=" OD1 ASP A 140 " model vdw 2.456 2.520 nonbonded pdb=" NH2 ARG A 65 " pdb=" OD1 ASP A 98 " model vdw 2.489 2.520 nonbonded pdb=" OG SER A 351 " pdb=" OE2 GGL A 501 " model vdw 2.499 2.440 nonbonded pdb=" OH TYR A 220 " pdb=" O PRO A 257 " model vdw 2.503 2.440 ... (remaining 28112 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 3.500 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.500 Find NCS groups from input model: 0.090 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:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 : 0.009 0.170 3379 Z= 0.581 Angle : 0.918 12.051 4588 Z= 0.502 Chirality : 0.051 0.294 499 Planarity : 0.005 0.045 585 Dihedral : 17.868 84.249 1277 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.15 % Allowed : 6.23 % Favored : 89.61 % 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: 0.64 (0.41), residues: 414 helix: 1.32 (0.35), residues: 210 sheet: -0.42 (0.72), residues: 64 loop : -0.42 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 263 HIS 0.008 0.002 HIS A 267 PHE 0.007 0.001 PHE A 381 TYR 0.009 0.001 TYR A 250 ARG 0.007 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 187 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8607 (ttp80) REVERT: A 263 TRP cc_start: 0.7802 (t-100) cc_final: 0.7316 (t-100) outliers start: 14 outliers final: 0 residues processed: 87 average time/residue: 1.5024 time to fit residues: 133.6740 Evaluate side-chains 54 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3379 Z= 0.199 Angle : 0.496 3.925 4588 Z= 0.261 Chirality : 0.044 0.142 499 Planarity : 0.005 0.046 585 Dihedral : 10.177 57.007 500 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.48 % Allowed : 14.54 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.42), residues: 414 helix: 2.05 (0.35), residues: 209 sheet: 0.64 (0.74), residues: 60 loop : -0.25 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 364 HIS 0.005 0.001 HIS A 388 PHE 0.010 0.002 PHE A 381 TYR 0.013 0.001 TYR A 363 ARG 0.005 0.001 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8856 (tttt) cc_final: 0.8655 (tttm) REVERT: A 153 MET cc_start: 0.9124 (mmp) cc_final: 0.8715 (mmp) REVERT: A 243 SER cc_start: 0.8905 (p) cc_final: 0.8612 (t) REVERT: A 259 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7613 (mt-10) outliers start: 5 outliers final: 0 residues processed: 62 average time/residue: 1.4577 time to fit residues: 92.6564 Evaluate side-chains 49 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.8612 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3379 Z= 0.161 Angle : 0.461 3.853 4588 Z= 0.241 Chirality : 0.042 0.128 499 Planarity : 0.004 0.046 585 Dihedral : 8.728 57.443 496 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.78 % Allowed : 16.62 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.43), residues: 414 helix: 2.25 (0.35), residues: 210 sheet: 0.61 (0.74), residues: 61 loop : -0.14 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 364 HIS 0.004 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.9124 (mmp) cc_final: 0.8678 (mmp) REVERT: A 256 ASP cc_start: 0.7808 (t70) cc_final: 0.7036 (t70) REVERT: A 259 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7761 (mt-10) outliers start: 6 outliers final: 0 residues processed: 59 average time/residue: 1.3583 time to fit residues: 82.2276 Evaluate side-chains 50 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3379 Z= 0.149 Angle : 0.445 4.032 4588 Z= 0.233 Chirality : 0.042 0.123 499 Planarity : 0.004 0.046 585 Dihedral : 8.215 58.310 496 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.37 % Allowed : 16.32 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.43), residues: 414 helix: 2.29 (0.35), residues: 210 sheet: 0.63 (0.73), residues: 61 loop : -0.01 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.008 0.002 HIS A 388 PHE 0.008 0.001 PHE A 7 TYR 0.009 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.397 Fit side-chains REVERT: A 153 MET cc_start: 0.9109 (mmp) cc_final: 0.8647 (mmp) REVERT: A 259 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7803 (mt-10) outliers start: 8 outliers final: 1 residues processed: 54 average time/residue: 1.3975 time to fit residues: 77.6398 Evaluate side-chains 47 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 0.0040 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3379 Z= 0.127 Angle : 0.428 4.099 4588 Z= 0.223 Chirality : 0.042 0.122 499 Planarity : 0.004 0.046 585 Dihedral : 8.011 59.690 496 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.19 % Allowed : 17.80 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.43), residues: 414 helix: 2.38 (0.35), residues: 211 sheet: 0.62 (0.74), residues: 59 loop : 0.00 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.003 0.001 HIS A 267 PHE 0.008 0.001 PHE A 341 TYR 0.006 0.001 TYR A 408 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.413 Fit side-chains REVERT: A 153 MET cc_start: 0.9110 (mmp) cc_final: 0.8648 (mmp) REVERT: A 256 ASP cc_start: 0.7663 (t70) cc_final: 0.7230 (t70) outliers start: 4 outliers final: 0 residues processed: 53 average time/residue: 1.4489 time to fit residues: 78.8355 Evaluate side-chains 50 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3379 Z= 0.168 Angle : 0.454 4.549 4588 Z= 0.237 Chirality : 0.043 0.122 499 Planarity : 0.004 0.047 585 Dihedral : 7.975 59.340 496 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.78 % Allowed : 18.69 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.43), residues: 414 helix: 2.31 (0.35), residues: 210 sheet: 0.75 (0.73), residues: 60 loop : 0.06 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 263 HIS 0.007 0.002 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.431 Fit side-chains REVERT: A 12 LYS cc_start: 0.8248 (mmtp) cc_final: 0.7998 (mmmt) REVERT: A 153 MET cc_start: 0.9108 (mmp) cc_final: 0.8697 (mmp) REVERT: A 256 ASP cc_start: 0.7596 (t70) cc_final: 0.6908 (t70) REVERT: A 259 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7771 (mp0) outliers start: 6 outliers final: 1 residues processed: 53 average time/residue: 1.4201 time to fit residues: 77.2431 Evaluate side-chains 51 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3379 Z= 0.265 Angle : 0.513 5.199 4588 Z= 0.269 Chirality : 0.045 0.147 499 Planarity : 0.005 0.048 585 Dihedral : 8.162 59.936 496 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.59 % Allowed : 18.99 % Favored : 80.42 % 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: 1.69 (0.43), residues: 414 helix: 2.12 (0.35), residues: 209 sheet: 0.77 (0.73), residues: 60 loop : -0.17 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 364 HIS 0.007 0.002 HIS A 388 PHE 0.012 0.002 PHE A 341 TYR 0.013 0.002 TYR A 363 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8270 (mmtp) cc_final: 0.7997 (mmmt) REVERT: A 246 ARG cc_start: 0.4987 (OUTLIER) cc_final: 0.4668 (mtp180) REVERT: A 256 ASP cc_start: 0.7546 (t70) cc_final: 0.6938 (t70) REVERT: A 259 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7807 (mp0) REVERT: A 302 THR cc_start: 0.8434 (p) cc_final: 0.8195 (t) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 1.3308 time to fit residues: 72.5695 Evaluate side-chains 54 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.8614 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3379 Z= 0.141 Angle : 0.454 5.674 4588 Z= 0.235 Chirality : 0.042 0.125 499 Planarity : 0.004 0.048 585 Dihedral : 7.809 59.342 496 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.19 % Allowed : 19.88 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.43), residues: 414 helix: 2.22 (0.35), residues: 210 sheet: 0.69 (0.74), residues: 59 loop : -0.07 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 263 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8274 (mmtp) cc_final: 0.8013 (mmmt) REVERT: A 259 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7853 (mp0) REVERT: A 302 THR cc_start: 0.8442 (p) cc_final: 0.8194 (t) outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 1.2917 time to fit residues: 73.1562 Evaluate side-chains 54 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3379 Z= 0.148 Angle : 0.471 6.650 4588 Z= 0.243 Chirality : 0.042 0.124 499 Planarity : 0.004 0.048 585 Dihedral : 7.751 59.763 496 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.59 % Allowed : 20.47 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.43), residues: 414 helix: 2.24 (0.35), residues: 210 sheet: 0.88 (0.74), residues: 58 loop : -0.02 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7981 (mmmt) REVERT: A 259 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7852 (mp0) REVERT: A 302 THR cc_start: 0.8426 (p) cc_final: 0.8176 (t) outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 1.3355 time to fit residues: 75.5516 Evaluate side-chains 55 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3379 Z= 0.149 Angle : 0.466 7.195 4588 Z= 0.239 Chirality : 0.042 0.122 499 Planarity : 0.004 0.048 585 Dihedral : 7.678 59.697 496 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.59 % Allowed : 20.18 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.43), residues: 414 helix: 2.23 (0.35), residues: 210 sheet: 0.91 (0.75), residues: 58 loop : -0.01 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.002 0.000 ARG A 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.412 Fit side-chains REVERT: A 12 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7978 (mmmt) REVERT: A 259 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7856 (mp0) REVERT: A 302 THR cc_start: 0.8413 (p) cc_final: 0.8161 (t) outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 1.3404 time to fit residues: 78.5840 Evaluate side-chains 55 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.077954 restraints weight = 4312.287| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 1.56 r_work: 0.2600 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3379 Z= 0.155 Angle : 0.470 7.621 4588 Z= 0.242 Chirality : 0.042 0.131 499 Planarity : 0.004 0.048 585 Dihedral : 7.692 59.611 496 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.30 % Allowed : 20.47 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.43), residues: 414 helix: 2.20 (0.35), residues: 210 sheet: 0.93 (0.75), residues: 58 loop : -0.00 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.002 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1875.58 seconds wall clock time: 34 minutes 1.16 seconds (2041.16 seconds total)