Starting phenix.real_space_refine on Sun Mar 10 19:42:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/03_2024/8dny_27584_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/03_2024/8dny_27584.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/03_2024/8dny_27584_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/03_2024/8dny_27584_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/03_2024/8dny_27584_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/03_2024/8dny_27584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/03_2024/8dny_27584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/03_2024/8dny_27584_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/03_2024/8dny_27584_trim_updated.pdb" } resolution = 2.85 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= 0.003 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 2869 2.51 5 N 694 2.21 5 O 742 1.98 5 H 5 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 4336 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3510 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 486 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 251 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "D" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 89 Unusual residues: {'T2X': 1, 'T3R': 2} Classifications: {'peptide': 7, 'undetermined': 3} Link IDs: {'NMTRANS': 1, 'TRANS': 3, None: 5} Not linked: pdbres="IML D 3 " pdbres="T2X D 4 " Not linked: pdbres="T2X D 4 " pdbres="YCP D 5 " Not linked: pdbres="HLX D 6 " pdbres="T3R D 7 " Not linked: pdbres="T3R D 7 " pdbres="NZC D 8 " Not linked: pdbres="YCP D 9 " pdbres="T3R D 10 " Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Planarities with less than four sites: {'IML:plan-1': 1, 'NZC:plan-1': 1, 'YCP:plan-1': 3, 'HLX:plan-1': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 3.10, per 1000 atoms: 0.71 Number of scatterers: 4336 At special positions: 0 Unit cell: (84, 76.65, 80.85, 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 26 16.00 O 742 8.00 N 694 7.00 C 2869 6.00 H 5 1.00 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 706.4 milliseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 1 sheets defined 66.8% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 106 through 133 Processing helix chain 'A' and resid 140 through 171 removed outlier: 6.084A pdb=" N ALA A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLY A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 196 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 242 through 259 Processing helix chain 'A' and resid 289 through 311 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 358 through 382 Processing helix chain 'A' and resid 387 through 397 removed outlier: 3.528A pdb=" N GLN A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 438 removed outlier: 3.782A pdb=" N ILE A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR A 410 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 412 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE A 417 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Proline residue: A 418 - end of helix removed outlier: 3.601A pdb=" N PHE A 423 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 438 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 467 Processing helix chain 'B' and resid 8 through 24 Processing helix chain 'B' and resid 30 through 65 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 70 through 95 Processing sheet with id= A, first strand: chain 'A' and resid 277 through 282 282 hydrogen bonds defined for protein. 783 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: 1.20 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.16: 5 1.16 - 1.32: 666 1.32 - 1.48: 1745 1.48 - 1.64: 1965 1.64 - 1.81: 43 Bond restraints: 4424 Sorted by residual: bond pdb=" C YCP D 2 " pdb=" N IML D 3 " ideal model delta sigma weight residual 1.329 1.548 -0.219 1.40e-02 5.10e+03 2.46e+02 bond pdb=" C YCP D 5 " pdb=" N HLX D 6 " ideal model delta sigma weight residual 1.329 1.516 -0.187 1.40e-02 5.10e+03 1.78e+02 bond pdb=" C ALA D 1 " pdb=" N YCP D 2 " ideal model delta sigma weight residual 1.329 1.509 -0.180 1.40e-02 5.10e+03 1.66e+02 bond pdb=" C NZC D 8 " pdb=" N YCP D 9 " ideal model delta sigma weight residual 1.329 1.497 -0.168 1.40e-02 5.10e+03 1.44e+02 bond pdb=" C35 T2X D 4 " pdb=" O77 T2X D 4 " ideal model delta sigma weight residual 1.401 1.182 0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 4419 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.17: 128 107.17 - 113.88: 2584 113.88 - 120.58: 1811 120.58 - 127.29: 1428 127.29 - 133.99: 35 Bond angle restraints: 5986 Sorted by residual: angle pdb=" N GLY A 442 " pdb=" CA GLY A 442 " pdb=" C GLY A 442 " ideal model delta sigma weight residual 115.08 107.70 7.38 1.19e+00 7.06e-01 3.84e+01 angle pdb=" N YCP D 9 " pdb=" CA YCP D 9 " pdb=" CB YCP D 9 " ideal model delta sigma weight residual 110.40 118.65 -8.25 1.50e+00 4.44e-01 3.03e+01 angle pdb=" C52 T3R D 10 " pdb=" N51 T3R D 10 " pdb=" C53 T3R D 10 " ideal model delta sigma weight residual 109.47 121.91 -12.44 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C29 T2X D 4 " pdb=" C35 T2X D 4 " pdb=" O77 T2X D 4 " ideal model delta sigma weight residual 108.35 119.26 -10.91 3.00e+00 1.11e-01 1.32e+01 angle pdb=" CA ALA D 1 " pdb=" C ALA D 1 " pdb=" N YCP D 2 " ideal model delta sigma weight residual 116.20 122.88 -6.68 2.00e+00 2.50e-01 1.11e+01 ... (remaining 5981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 2514 24.87 - 49.73: 100 49.73 - 74.60: 8 74.60 - 99.46: 5 99.46 - 124.33: 1 Dihedral angle restraints: 2628 sinusoidal: 1041 harmonic: 1587 Sorted by residual: dihedral pdb=" CB YCP D 9 " pdb=" CG YCP D 9 " pdb=" CD YCP D 9 " pdb=" CE YCP D 9 " ideal model delta sinusoidal sigma weight residual -64.18 60.15 -124.33 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" CA ASN A 241 " pdb=" C ASN A 241 " pdb=" N LEU A 242 " pdb=" CA LEU A 242 " ideal model delta harmonic sigma weight residual 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA THR A 286 " pdb=" C THR A 286 " pdb=" N SER A 287 " pdb=" CA SER A 287 " ideal model delta harmonic sigma weight residual -180.00 -164.17 -15.83 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 2625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 525 0.045 - 0.091: 148 0.091 - 0.136: 25 0.136 - 0.182: 3 0.182 - 0.227: 5 Chirality restraints: 706 Sorted by residual: chirality pdb=" CA YCP D 2 " pdb=" N YCP D 2 " pdb=" C YCP D 2 " pdb=" CB YCP D 2 " both_signs ideal model delta sigma weight residual False 2.48 2.71 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB IML D 3 " pdb=" CA IML D 3 " pdb=" CG1 IML D 3 " pdb=" CG2 IML D 3 " both_signs ideal model delta sigma weight residual False 2.56 2.79 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ALA D 1 " pdb=" N ALA D 1 " pdb=" C ALA D 1 " pdb=" CB ALA D 1 " both_signs ideal model delta sigma weight residual False 2.48 2.70 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 703 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 386 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 387 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 289 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 290 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 105 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 106 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " 0.026 5.00e-02 4.00e+02 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.49: 18 2.49 - 3.02: 2612 3.02 - 3.54: 5572 3.54 - 4.07: 7616 4.07 - 4.60: 11889 Nonbonded interactions: 27707 Sorted by model distance: nonbonded pdb=" H ALA D 1 " pdb=" O NZC D 8 " model vdw 1.962 1.850 nonbonded pdb=" N GLY A 74 " pdb=" OE1 GLU A 78 " model vdw 2.287 2.350 nonbonded pdb=" OG SER A 58 " pdb=" NH2 ARG A 73 " model vdw 2.291 2.350 nonbonded pdb=" O ARG A 236 " pdb=" ND2 ASN A 241 " model vdw 2.296 2.350 nonbonded pdb=" NH2 ARG A 205 " pdb=" OE1 GLU A 232 " model vdw 2.297 2.350 ... (remaining 27702 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: 1.430 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: 0.080 Extract box with map and model: 3.610 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.160 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 0.219 4419 Z= 0.592 Angle : 0.683 12.439 5976 Z= 0.344 Chirality : 0.044 0.227 706 Planarity : 0.005 0.050 726 Dihedral : 13.548 124.326 1606 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 2.03 (0.36), residues: 541 helix: 2.13 (0.25), residues: 402 sheet: -2.20 (1.14), residues: 12 loop : -0.86 (0.54), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.009 0.001 PHE A 252 TYR 0.005 0.001 TYR A 285 ARG 0.001 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.532 Fit side-chains REVERT: A 389 ASP cc_start: 0.7575 (m-30) cc_final: 0.7353 (m-30) REVERT: C 76 MET cc_start: 0.6679 (mtt) cc_final: 0.6452 (mtp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 1.4721 time to fit residues: 104.8205 Evaluate side-chains 49 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 49 optimal weight: 0.5980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 237 GLN A 465 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4419 Z= 0.144 Angle : 0.403 4.578 5976 Z= 0.215 Chirality : 0.035 0.127 706 Planarity : 0.005 0.043 726 Dihedral : 8.117 97.773 628 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.53 % Allowed : 8.28 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.37), residues: 541 helix: 2.44 (0.26), residues: 399 sheet: -1.76 (1.36), residues: 12 loop : -0.62 (0.55), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.007 0.001 PHE B 33 TYR 0.007 0.001 TYR A 263 ARG 0.001 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.471 Fit side-chains REVERT: A 30 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7057 (pt0) REVERT: A 381 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: C 76 MET cc_start: 0.6745 (mtt) cc_final: 0.6491 (mtp) outliers start: 7 outliers final: 3 residues processed: 56 average time/residue: 1.4475 time to fit residues: 83.8569 Evaluate side-chains 49 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 385 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.0010 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4419 Z= 0.245 Angle : 0.448 5.013 5976 Z= 0.235 Chirality : 0.037 0.128 706 Planarity : 0.004 0.039 726 Dihedral : 7.161 81.265 628 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.53 % Allowed : 9.59 % Favored : 88.89 % 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: 2.33 (0.38), residues: 541 helix: 2.26 (0.26), residues: 403 sheet: -1.67 (1.51), residues: 12 loop : -0.52 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.003 0.001 HIS B 58 PHE 0.010 0.001 PHE B 49 TYR 0.008 0.001 TYR A 263 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.504 Fit side-chains REVERT: A 30 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7099 (mt-10) REVERT: C 76 MET cc_start: 0.6751 (mtt) cc_final: 0.6505 (mtp) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 1.5204 time to fit residues: 86.9037 Evaluate side-chains 58 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 385 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4419 Z= 0.171 Angle : 0.401 4.655 5976 Z= 0.210 Chirality : 0.036 0.126 706 Planarity : 0.004 0.040 726 Dihedral : 6.564 73.226 628 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.31 % Allowed : 12.20 % Favored : 86.49 % 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: 2.65 (0.38), residues: 541 helix: 2.48 (0.26), residues: 403 sheet: -1.59 (1.55), residues: 12 loop : -0.31 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 34 HIS 0.002 0.001 HIS A 360 PHE 0.007 0.001 PHE A 423 TYR 0.006 0.001 TYR A 263 ARG 0.001 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.525 Fit side-chains REVERT: A 30 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: C 76 MET cc_start: 0.6734 (mtt) cc_final: 0.6519 (mtp) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 1.3555 time to fit residues: 73.0210 Evaluate side-chains 51 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 385 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 chunk 45 optimal weight: 0.0030 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4419 Z= 0.224 Angle : 0.434 4.782 5976 Z= 0.225 Chirality : 0.037 0.124 706 Planarity : 0.004 0.041 726 Dihedral : 6.055 61.755 628 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.61 % Allowed : 11.55 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.38), residues: 541 helix: 2.41 (0.26), residues: 403 sheet: -1.69 (1.50), residues: 12 loop : -0.29 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.003 0.001 HIS B 58 PHE 0.010 0.001 PHE B 49 TYR 0.008 0.001 TYR A 263 ARG 0.001 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.481 Fit side-chains REVERT: A 30 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7090 (mt-10) REVERT: C 76 MET cc_start: 0.6818 (mtt) cc_final: 0.6584 (mtt) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 1.3236 time to fit residues: 78.2591 Evaluate side-chains 51 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 385 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.0040 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.0070 chunk 51 optimal weight: 0.0970 overall best weight: 0.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4419 Z= 0.093 Angle : 0.359 4.456 5976 Z= 0.188 Chirality : 0.035 0.126 706 Planarity : 0.004 0.043 726 Dihedral : 4.637 44.057 628 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.09 % Allowed : 12.85 % Favored : 86.06 % 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: 3.12 (0.39), residues: 541 helix: 2.86 (0.27), residues: 402 sheet: -2.20 (1.16), residues: 18 loop : -0.02 (0.62), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.001 0.000 HIS A 360 PHE 0.006 0.001 PHE A 156 TYR 0.004 0.000 TYR A 263 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.483 Fit side-chains REVERT: A 25 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7591 (ttpt) REVERT: A 389 ASP cc_start: 0.7430 (m-30) cc_final: 0.7205 (m-30) REVERT: C 76 MET cc_start: 0.6731 (mtt) cc_final: 0.6475 (mtp) outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 1.2658 time to fit residues: 67.1670 Evaluate side-chains 49 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 385 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 0.0770 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4419 Z= 0.162 Angle : 0.388 4.669 5976 Z= 0.202 Chirality : 0.035 0.125 706 Planarity : 0.004 0.043 726 Dihedral : 4.252 41.603 628 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.87 % Allowed : 13.94 % Favored : 85.19 % 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: 3.07 (0.38), residues: 541 helix: 2.84 (0.27), residues: 402 sheet: -2.37 (1.12), residues: 18 loop : -0.09 (0.62), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 34 HIS 0.003 0.001 HIS B 58 PHE 0.008 0.001 PHE B 49 TYR 0.006 0.001 TYR A 263 ARG 0.001 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.478 Fit side-chains REVERT: A 389 ASP cc_start: 0.7479 (m-30) cc_final: 0.7211 (m-30) REVERT: C 76 MET cc_start: 0.6736 (mtt) cc_final: 0.6494 (mtp) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 1.2104 time to fit residues: 63.0027 Evaluate side-chains 50 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 428 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4419 Z= 0.194 Angle : 0.408 4.687 5976 Z= 0.212 Chirality : 0.036 0.125 706 Planarity : 0.004 0.043 726 Dihedral : 4.425 40.147 628 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.87 % Allowed : 13.94 % Favored : 85.19 % 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: 2.92 (0.38), residues: 541 helix: 2.74 (0.26), residues: 402 sheet: -2.48 (1.09), residues: 18 loop : -0.18 (0.62), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.003 0.001 HIS B 58 PHE 0.008 0.001 PHE B 49 TYR 0.006 0.001 TYR A 263 ARG 0.001 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.503 Fit side-chains REVERT: A 389 ASP cc_start: 0.7499 (m-30) cc_final: 0.7206 (m-30) REVERT: C 76 MET cc_start: 0.6805 (mtt) cc_final: 0.6539 (mtp) outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 1.2489 time to fit residues: 66.2470 Evaluate side-chains 49 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 428 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4419 Z= 0.235 Angle : 0.429 4.808 5976 Z= 0.223 Chirality : 0.036 0.124 706 Planarity : 0.004 0.043 726 Dihedral : 4.580 40.069 628 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.09 % Allowed : 14.38 % Favored : 84.53 % 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: 2.76 (0.38), residues: 541 helix: 2.63 (0.26), residues: 402 sheet: -2.62 (1.07), residues: 18 loop : -0.27 (0.61), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.003 0.001 HIS B 58 PHE 0.012 0.001 PHE A 312 TYR 0.007 0.001 TYR A 263 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.489 Fit side-chains REVERT: A 389 ASP cc_start: 0.7547 (m-30) cc_final: 0.7290 (m-30) REVERT: C 76 MET cc_start: 0.6821 (mtt) cc_final: 0.6584 (mtt) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 1.2873 time to fit residues: 72.1739 Evaluate side-chains 49 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4419 Z= 0.177 Angle : 0.403 4.644 5976 Z= 0.210 Chirality : 0.036 0.125 706 Planarity : 0.004 0.043 726 Dihedral : 4.494 39.543 628 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.87 % Allowed : 14.81 % Favored : 84.31 % 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: 2.85 (0.38), residues: 541 helix: 2.70 (0.26), residues: 402 sheet: -2.53 (1.08), residues: 18 loop : -0.24 (0.62), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.015 0.001 PHE A 312 TYR 0.006 0.001 TYR A 263 ARG 0.001 0.000 ARG A 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.468 Fit side-chains REVERT: A 389 ASP cc_start: 0.7503 (m-30) cc_final: 0.7194 (m-30) REVERT: C 76 MET cc_start: 0.6797 (mtt) cc_final: 0.6571 (mtt) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 1.1135 time to fit residues: 55.8514 Evaluate side-chains 49 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 0.0030 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.166173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131025 restraints weight = 4661.872| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.67 r_work: 0.3462 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4419 Z= 0.144 Angle : 0.380 4.592 5976 Z= 0.198 Chirality : 0.035 0.125 706 Planarity : 0.004 0.043 726 Dihedral : 4.297 37.524 628 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.09 % Allowed : 14.81 % Favored : 84.10 % 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: 3.05 (0.39), residues: 541 helix: 2.85 (0.27), residues: 402 sheet: -2.46 (1.10), residues: 18 loop : -0.19 (0.62), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.014 0.001 PHE A 312 TYR 0.005 0.001 TYR A 263 ARG 0.001 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1936.37 seconds wall clock time: 35 minutes 8.47 seconds (2108.47 seconds total)