Starting phenix.real_space_refine on Sun Mar 10 16:34:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcy_38259/03_2024/8xcy_38259_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcy_38259/03_2024/8xcy_38259.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcy_38259/03_2024/8xcy_38259_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcy_38259/03_2024/8xcy_38259_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcy_38259/03_2024/8xcy_38259_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcy_38259/03_2024/8xcy_38259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcy_38259/03_2024/8xcy_38259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcy_38259/03_2024/8xcy_38259_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcy_38259/03_2024/8xcy_38259_neut_updated.pdb" } resolution = 2.91 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 563 2.21 5 O 632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 78": "OE1" <-> "OE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A ASP 390": "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: 3311 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3262 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3254 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 416, 3254 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3317 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 49 Unusual residues: {'NAP': 1} Classifications: {'peptide': 1, 'undetermined': 1, 'water': 8} Link IDs: {None: 9} 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: 3.86, per 1000 atoms: 1.17 Number of scatterers: 3311 At special positions: 0 Unit cell: (68.432, 72.944, 72.192, 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 632 8.00 N 563 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: 1.19 Conformation dependent library (CDL) restraints added in 1.2 seconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 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 48.1% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.922A 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: 3.529A 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: 5.725A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.308A 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 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: 3.853A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 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: 4.722A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.458A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 248 through 250 Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.730A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 160 hydrogen bonds defined for protein. 465 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: 0.81 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1071 1.34 - 1.46: 659 1.46 - 1.58: 1618 1.58 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3377 Sorted by residual: bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.569 0.167 2.00e-02 2.50e+03 7.01e+01 bond pdb=" C ARG A 187 " pdb=" CA BARG A 187 " ideal model delta sigma weight residual 1.522 1.440 0.082 1.34e-02 5.57e+03 3.76e+01 bond pdb=" C4A NAP A 500 " pdb=" N3A NAP A 500 " ideal model delta sigma weight residual 1.332 1.440 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C6A NAP A 500 " pdb=" N6A NAP A 500 " ideal model delta sigma weight residual 1.335 1.438 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C8A NAP A 500 " pdb=" N7A NAP A 500 " ideal model delta sigma weight residual 1.301 1.398 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 3372 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.23: 94 106.23 - 113.18: 1850 113.18 - 120.14: 1168 120.14 - 127.09: 1421 127.09 - 134.04: 52 Bond angle restraints: 4585 Sorted by residual: angle pdb=" C ASP A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta sigma weight residual 119.84 127.09 -7.25 1.25e+00 6.40e-01 3.37e+01 angle pdb=" O1A NAP A 500 " pdb=" PA NAP A 500 " pdb=" O2A NAP A 500 " ideal model delta sigma weight residual 121.77 109.65 12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O1N NAP A 500 " pdb=" PN NAP A 500 " pdb=" O2N NAP A 500 " ideal model delta sigma weight residual 122.51 110.63 11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 123.05 127.91 -4.86 1.57e+00 4.06e-01 9.59e+00 angle pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " pdb=" O2X NAP A 500 " ideal model delta sigma weight residual 100.14 109.28 -9.14 3.00e+00 1.11e-01 9.29e+00 ... (remaining 4580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 1785 17.55 - 35.09: 181 35.09 - 52.64: 48 52.64 - 70.19: 21 70.19 - 87.74: 7 Dihedral angle restraints: 2042 sinusoidal: 847 harmonic: 1195 Sorted by residual: dihedral pdb=" CB GLU A 78 " pdb=" CG GLU A 78 " pdb=" CD GLU A 78 " pdb=" OE1 GLU A 78 " ideal model delta sinusoidal sigma weight residual 0.00 -84.53 84.53 1 3.00e+01 1.11e-03 9.65e+00 dihedral pdb=" N ARG A 246 " pdb=" CA ARG A 246 " pdb=" CB ARG A 246 " pdb=" CG ARG A 246 " ideal model delta sinusoidal sigma weight residual -180.00 -121.63 -58.37 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N ILE A 297 " pdb=" CA ILE A 297 " pdb=" CB ILE A 297 " pdb=" CG1 ILE A 297 " ideal model delta sinusoidal sigma weight residual -180.00 -122.58 -57.42 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 2039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 416 0.059 - 0.118: 77 0.118 - 0.177: 5 0.177 - 0.236: 0 0.236 - 0.295: 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=" CB VAL A 97 " pdb=" CA VAL A 97 " pdb=" CG1 VAL A 97 " pdb=" CG2 VAL A 97 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CA MET A 164 " pdb=" N MET A 164 " pdb=" C MET A 164 " pdb=" CB MET A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 496 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO A 150 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO A 142 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 323 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO A 324 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.021 5.00e-02 4.00e+02 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 630 2.77 - 3.30: 3194 3.30 - 3.84: 5752 3.84 - 4.37: 6969 4.37 - 4.90: 11771 Nonbonded interactions: 28316 Sorted by model distance: nonbonded pdb=" CG TRP A 30 " pdb=" NE1 TRP A 30 " model vdw 2.241 2.672 nonbonded pdb=" NZ LYS A 93 " pdb=" OD1 ASN A 344 " model vdw 2.301 2.520 nonbonded pdb=" OG SER A 243 " pdb=" OD1 ASN A 281 " model vdw 2.331 2.440 nonbonded pdb=" N THR A 280 " pdb=" OE2 GLU A 283 " model vdw 2.405 2.520 nonbonded pdb=" O1N NAP A 500 " pdb=" O2A NAP A 500 " model vdw 2.437 3.040 ... (remaining 28311 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=0.50 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.570 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.830 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.008 0.167 3377 Z= 0.522 Angle : 0.830 12.117 4585 Z= 0.440 Chirality : 0.046 0.295 499 Planarity : 0.004 0.049 584 Dihedral : 17.011 87.736 1280 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.56 % Allowed : 2.08 % Favored : 94.36 % 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: 0.91 (0.42), residues: 415 helix: 2.09 (0.35), residues: 208 sheet: -0.85 (0.64), residues: 65 loop : -0.92 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.377 Fit side-chains REVERT: A 256 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.7037 (t0) REVERT: A 263 TRP cc_start: 0.7389 (t-100) cc_final: 0.6941 (t-100) REVERT: A 383 GLU cc_start: 0.7670 (tp30) cc_final: 0.7438 (tp30) outliers start: 12 outliers final: 1 residues processed: 86 average time/residue: 1.3013 time to fit residues: 114.8398 Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 298 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 281 ASN A 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3377 Z= 0.167 Angle : 0.498 8.082 4585 Z= 0.259 Chirality : 0.042 0.158 499 Planarity : 0.004 0.047 584 Dihedral : 11.536 59.985 500 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.08 % Allowed : 12.17 % Favored : 85.76 % 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: 1.42 (0.43), residues: 415 helix: 2.49 (0.36), residues: 206 sheet: -0.93 (0.64), residues: 70 loop : -0.38 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 253 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6497 (p0) REVERT: A 263 TRP cc_start: 0.7376 (t-100) cc_final: 0.6954 (t-100) REVERT: A 287 LEU cc_start: 0.9038 (mp) cc_final: 0.8817 (mp) outliers start: 7 outliers final: 1 residues processed: 65 average time/residue: 1.2020 time to fit residues: 80.4653 Evaluate side-chains 56 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 332 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 10.0000 chunk 11 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3377 Z= 0.144 Angle : 0.457 6.306 4585 Z= 0.238 Chirality : 0.041 0.144 499 Planarity : 0.004 0.047 584 Dihedral : 10.434 58.028 495 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.37 % Allowed : 14.24 % Favored : 83.38 % 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: 1.57 (0.43), residues: 415 helix: 2.63 (0.36), residues: 206 sheet: -0.68 (0.65), residues: 72 loop : -0.43 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.381 Fit side-chains REVERT: A 45 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: A 253 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6457 (p0) REVERT: A 263 TRP cc_start: 0.7429 (t-100) cc_final: 0.6986 (t-100) REVERT: A 375 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7652 (mtmt) REVERT: A 383 GLU cc_start: 0.7612 (tp30) cc_final: 0.7332 (tp30) outliers start: 8 outliers final: 1 residues processed: 60 average time/residue: 1.2397 time to fit residues: 76.5608 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3377 Z= 0.120 Angle : 0.426 5.017 4585 Z= 0.224 Chirality : 0.041 0.129 499 Planarity : 0.004 0.047 584 Dihedral : 9.619 59.458 495 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.08 % Allowed : 14.84 % Favored : 83.09 % 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: 1.65 (0.43), residues: 415 helix: 2.68 (0.35), residues: 207 sheet: -0.70 (0.66), residues: 72 loop : -0.35 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS A 388 PHE 0.007 0.001 PHE A 381 TYR 0.010 0.001 TYR A 408 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.382 Fit side-chains REVERT: A 253 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6486 (p0) REVERT: A 263 TRP cc_start: 0.7449 (t-100) cc_final: 0.7018 (t-100) REVERT: A 375 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7691 (mtmt) outliers start: 7 outliers final: 1 residues processed: 59 average time/residue: 1.2092 time to fit residues: 73.6125 Evaluate side-chains 55 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 0.0270 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3377 Z= 0.153 Angle : 0.452 5.302 4585 Z= 0.237 Chirality : 0.041 0.136 499 Planarity : 0.004 0.047 584 Dihedral : 8.949 58.915 495 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.78 % Allowed : 15.43 % Favored : 82.79 % 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: 1.56 (0.43), residues: 415 helix: 2.65 (0.35), residues: 207 sheet: -0.78 (0.65), residues: 72 loop : -0.45 (0.54), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.012 0.001 TYR A 408 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.389 Fit side-chains REVERT: A 16 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7537 (tmm-80) REVERT: A 263 TRP cc_start: 0.7481 (t-100) cc_final: 0.7101 (t-100) REVERT: A 282 GLU cc_start: 0.8277 (mp0) cc_final: 0.7709 (mt-10) REVERT: A 308 ASN cc_start: 0.7563 (m-40) cc_final: 0.7298 (m-40) REVERT: A 375 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7693 (mtmt) outliers start: 6 outliers final: 2 residues processed: 61 average time/residue: 1.1952 time to fit residues: 75.1344 Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 0.2980 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3377 Z= 0.250 Angle : 0.512 7.837 4585 Z= 0.264 Chirality : 0.044 0.157 499 Planarity : 0.004 0.047 584 Dihedral : 8.347 58.547 495 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.08 % Allowed : 14.84 % Favored : 83.09 % 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: 1.30 (0.43), residues: 415 helix: 2.52 (0.35), residues: 206 sheet: -0.97 (0.63), residues: 72 loop : -0.66 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.015 0.001 TYR A 408 ARG 0.002 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.418 Fit side-chains REVERT: A 16 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7564 (tmm-80) REVERT: A 78 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: A 263 TRP cc_start: 0.7390 (t-100) cc_final: 0.7185 (t-100) REVERT: A 282 GLU cc_start: 0.8217 (mp0) cc_final: 0.7664 (mt-10) REVERT: A 308 ASN cc_start: 0.7575 (m-40) cc_final: 0.7296 (m-40) REVERT: A 375 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7666 (mtmt) outliers start: 7 outliers final: 2 residues processed: 60 average time/residue: 1.2977 time to fit residues: 80.0987 Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 375 LYS 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: 4.9990 chunk 33 optimal weight: 0.0570 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 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: 0.8389 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3377 Z= 0.209 Angle : 0.487 8.328 4585 Z= 0.254 Chirality : 0.043 0.146 499 Planarity : 0.004 0.047 584 Dihedral : 8.050 58.231 495 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.08 % Allowed : 16.62 % 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: 1.26 (0.42), residues: 415 helix: 2.44 (0.35), residues: 206 sheet: -0.50 (0.70), residues: 62 loop : -0.90 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.013 0.001 TYR A 408 ARG 0.001 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.378 Fit side-chains REVERT: A 16 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7551 (tmm-80) REVERT: A 259 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6766 (mm-30) REVERT: A 263 TRP cc_start: 0.7402 (t-100) cc_final: 0.7164 (t-100) REVERT: A 282 GLU cc_start: 0.8108 (mp0) cc_final: 0.7488 (mt-10) REVERT: A 308 ASN cc_start: 0.7508 (m-40) cc_final: 0.7242 (m-40) REVERT: A 375 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7676 (mtmt) outliers start: 7 outliers final: 2 residues processed: 60 average time/residue: 1.3052 time to fit residues: 80.6295 Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3377 Z= 0.192 Angle : 0.483 6.531 4585 Z= 0.252 Chirality : 0.043 0.140 499 Planarity : 0.004 0.048 584 Dihedral : 7.427 59.974 495 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.08 % Allowed : 17.51 % 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: 1.25 (0.42), residues: 415 helix: 2.45 (0.35), residues: 206 sheet: -0.61 (0.68), residues: 62 loop : -0.89 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.012 0.001 TYR A 408 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.557 Fit side-chains REVERT: A 16 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7560 (tmm-80) REVERT: A 259 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6766 (mm-30) REVERT: A 263 TRP cc_start: 0.7405 (t-100) cc_final: 0.7205 (t-100) REVERT: A 282 GLU cc_start: 0.8134 (mp0) cc_final: 0.7463 (mt-10) REVERT: A 287 LEU cc_start: 0.8705 (mp) cc_final: 0.8326 (pt) REVERT: A 308 ASN cc_start: 0.7479 (m-40) cc_final: 0.7212 (m-40) REVERT: A 375 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7680 (mtmt) outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 1.3362 time to fit residues: 82.4868 Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.0570 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3377 Z= 0.155 Angle : 0.455 6.528 4585 Z= 0.239 Chirality : 0.042 0.130 499 Planarity : 0.004 0.048 584 Dihedral : 6.832 59.304 495 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.19 % Allowed : 18.10 % Favored : 80.71 % 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: 1.33 (0.43), residues: 415 helix: 2.46 (0.35), residues: 207 sheet: -0.76 (0.68), residues: 66 loop : -0.66 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.012 0.001 TYR A 408 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.377 Fit side-chains REVERT: A 16 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7542 (tmm-80) REVERT: A 259 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6747 (mm-30) REVERT: A 263 TRP cc_start: 0.7457 (t-100) cc_final: 0.7190 (t-100) REVERT: A 282 GLU cc_start: 0.8057 (mp0) cc_final: 0.7398 (mt-10) REVERT: A 308 ASN cc_start: 0.7451 (m-40) cc_final: 0.7198 (m-40) REVERT: A 375 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7688 (mtmt) outliers start: 4 outliers final: 1 residues processed: 57 average time/residue: 1.2287 time to fit residues: 72.1928 Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 40.0000 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3377 Z= 0.223 Angle : 0.493 5.741 4585 Z= 0.258 Chirality : 0.043 0.147 499 Planarity : 0.004 0.048 584 Dihedral : 6.810 59.107 495 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.48 % Allowed : 18.40 % Favored : 80.12 % 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: 1.26 (0.43), residues: 415 helix: 2.42 (0.35), residues: 207 sheet: -0.84 (0.67), residues: 66 loop : -0.70 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.016 0.001 TYR A 408 ARG 0.001 0.000 ARG A 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.398 Fit side-chains REVERT: A 16 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7561 (tmm-80) REVERT: A 259 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6782 (mm-30) REVERT: A 263 TRP cc_start: 0.7398 (t-100) cc_final: 0.7198 (t-100) REVERT: A 282 GLU cc_start: 0.8098 (mp0) cc_final: 0.7388 (mt-10) REVERT: A 308 ASN cc_start: 0.7437 (m-40) cc_final: 0.7163 (m-40) REVERT: A 375 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7679 (mtmt) outliers start: 5 outliers final: 2 residues processed: 56 average time/residue: 1.3235 time to fit residues: 76.2589 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.102437 restraints weight = 6414.231| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.99 r_work: 0.2888 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3377 Z= 0.218 Angle : 0.484 5.820 4585 Z= 0.254 Chirality : 0.043 0.146 499 Planarity : 0.004 0.048 584 Dihedral : 6.842 59.098 495 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.19 % Allowed : 18.40 % 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: 1.35 (0.42), residues: 415 helix: 2.51 (0.35), residues: 201 sheet: -0.96 (0.62), residues: 76 loop : -0.38 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.008 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.016 0.001 TYR A 408 ARG 0.001 0.000 ARG A 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1879.65 seconds wall clock time: 34 minutes 3.26 seconds (2043.26 seconds total)