Starting phenix.real_space_refine on Thu Dec 7 20:39:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/12_2023/8dny_27584_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/12_2023/8dny_27584.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/12_2023/8dny_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_27584/12_2023/8dny_27584_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/12_2023/8dny_27584_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/12_2023/8dny_27584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/12_2023/8dny_27584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/12_2023/8dny_27584_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dny_27584/12_2023/8dny_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-1.21rc1-5172/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: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'NZC:plan-1': 1, 'IML:plan-1': 1, 'T2X:plan-1': 1, 'T3R:plan-1': 2, 'HLX:plan-1': 1, 'YCP:plan-1': 3} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 3.00, per 1000 atoms: 0.69 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: 2.04 Conformation dependent library (CDL) restraints added in 823.4 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: 0.79 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: 1.08 Time building geometry restraints manager: 2.17 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=" N ALA D 1 " pdb=" H ALA D 1 " ideal model delta sigma weight residual 0.860 0.998 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (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=" 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 angle pdb=" N ILE A 441 " pdb=" CA ILE A 441 " pdb=" C ILE A 441 " ideal model delta sigma weight residual 109.21 104.96 4.25 1.36e+00 5.41e-01 9.77e+00 ... (remaining 5981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 2563 33.38 - 66.76: 47 66.76 - 100.14: 11 100.14 - 133.52: 3 133.52 - 166.89: 4 Dihedral angle restraints: 2628 sinusoidal: 1041 harmonic: 1587 Sorted by residual: dihedral pdb=" C30 T2X D 4 " pdb=" C31 T2X D 4 " pdb=" C32 T2X D 4 " pdb=" C33 T2X D 4 " ideal model delta sinusoidal sigma weight residual -119.91 46.98 -166.89 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C30 T2X D 4 " pdb=" C31 T2X D 4 " pdb=" C32 T2X D 4 " pdb=" C34 T2X D 4 " ideal model delta sinusoidal sigma weight residual 120.09 -77.96 -161.95 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C52 T3R D 10 " pdb=" C53 T3R D 10 " pdb=" N51 T3R D 10 " pdb=" C54 T3R D 10 " ideal model delta sinusoidal sigma weight residual 76.03 -85.07 161.10 1 3.00e+01 1.11e-03 2.08e+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: 0.010 Normalize map: mean=0, sd=1: 0.630 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: 0.130 Extract box with map and model: 3.640 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.640 Find NCS groups from input model: 0.300 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: 33.640 ------------------------------------------------------------------------------- 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 : 0.008 0.219 4419 Z= 0.587 Angle : 0.676 12.439 5976 Z= 0.343 Chirality : 0.044 0.227 706 Planarity : 0.005 0.050 726 Dihedral : 17.138 166.894 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 : 0.522 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 1.3971 time to fit residues: 99.6687 Evaluate side-chains 49 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6773 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.4176 ------------------------------------------------------------------------------- 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: 0.7700 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4419 Z= 0.135 Angle : 0.399 4.578 5976 Z= 0.212 Chirality : 0.035 0.126 706 Planarity : 0.005 0.041 726 Dihedral : 15.124 141.430 628 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.53 % Allowed : 8.50 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.37), residues: 541 helix: 2.47 (0.26), residues: 399 sheet: -1.75 (1.35), residues: 12 loop : -0.60 (0.55), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.007 0.001 PHE B 33 TYR 0.006 0.001 TYR A 263 ARG 0.001 0.000 ARG A 388 *********************** 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 : 0.496 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 56 average time/residue: 1.3731 time to fit residues: 79.6285 Evaluate side-chains 51 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.0770 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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: 0.7746 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4419 Z= 0.183 Angle : 0.417 4.956 5976 Z= 0.218 Chirality : 0.036 0.126 706 Planarity : 0.004 0.040 726 Dihedral : 11.739 101.310 628 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.53 % Allowed : 9.80 % Favored : 88.67 % 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: 2.61 (0.38), residues: 541 helix: 2.48 (0.26), residues: 403 sheet: -1.70 (1.47), residues: 12 loop : -0.43 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.003 0.001 HIS B 58 PHE 0.010 0.001 PHE A 375 TYR 0.006 0.001 TYR A 263 ARG 0.001 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 56 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.516 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 1.2811 time to fit residues: 71.8555 Evaluate side-chains 54 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.1004 time to fit residues: 0.8428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.7778 moved from start: 0.1624 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= 0.225 Angle : 0.437 4.912 5976 Z= 0.227 Chirality : 0.036 0.125 706 Planarity : 0.004 0.041 726 Dihedral : 10.281 88.586 628 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.74 % Allowed : 11.55 % Favored : 86.71 % 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: 2.55 (0.38), residues: 541 helix: 2.41 (0.26), residues: 403 sheet: -1.59 (1.54), residues: 12 loop : -0.38 (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 0.009 0.001 PHE B 49 TYR 0.008 0.001 TYR A 263 ARG 0.001 0.000 ARG A 236 *********************** 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 56 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.571 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 1.2397 time to fit residues: 69.6824 Evaluate side-chains 53 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.502 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 1.5715 time to fit residues: 2.3116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- 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: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4419 Z= 0.232 Angle : 0.432 4.755 5976 Z= 0.225 Chirality : 0.037 0.125 706 Planarity : 0.004 0.039 726 Dihedral : 9.883 88.040 628 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.53 % Allowed : 12.42 % 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: 2.52 (0.38), residues: 541 helix: 2.41 (0.26), residues: 403 sheet: -1.91 (1.42), residues: 12 loop : -0.41 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.003 0.001 HIS A 360 PHE 0.009 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 55 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.492 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 55 average time/residue: 1.3085 time to fit residues: 74.8126 Evaluate side-chains 50 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.7419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.0060 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.2594 ------------------------------------------------------------------------------- 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: 0.7726 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4419 Z= 0.104 Angle : 0.364 4.515 5976 Z= 0.190 Chirality : 0.035 0.126 706 Planarity : 0.004 0.043 726 Dihedral : 8.953 78.426 628 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.53 % Allowed : 13.29 % 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 (0.39), residues: 541 helix: 2.84 (0.27), residues: 402 sheet: -2.39 (1.09), residues: 18 loop : -0.12 (0.62), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.001 0.000 HIS A 360 PHE 0.007 0.001 PHE A 312 TYR 0.005 0.000 TYR A 263 ARG 0.001 0.000 ARG A 231 *********************** 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 54 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.476 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 1.3258 time to fit residues: 70.3021 Evaluate side-chains 51 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1008 time to fit residues: 0.8445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7769 moved from start: 0.1907 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= 0.197 Angle : 0.413 4.685 5976 Z= 0.213 Chirality : 0.036 0.124 706 Planarity : 0.004 0.039 726 Dihedral : 8.921 77.476 628 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.09 % Allowed : 13.94 % Favored : 84.97 % 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: 2.90 (0.38), residues: 541 helix: 2.73 (0.26), residues: 402 sheet: -2.62 (1.04), residues: 18 loop : -0.20 (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 0.009 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 51 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.522 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 1.2625 time to fit residues: 65.9877 Evaluate side-chains 50 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.6965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 33 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 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: 0.7771 moved from start: 0.1974 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= 0.193 Angle : 0.410 4.669 5976 Z= 0.212 Chirality : 0.036 0.125 706 Planarity : 0.004 0.039 726 Dihedral : 8.687 71.956 628 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.31 % Allowed : 13.94 % Favored : 84.75 % 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: -2.65 (1.04), residues: 18 loop : -0.23 (0.62), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 34 HIS 0.002 0.001 HIS B 58 PHE 0.008 0.001 PHE B 49 TYR 0.007 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 53 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.557 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 1.2313 time to fit residues: 66.7180 Evaluate side-chains 49 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.6832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 0.0470 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 0.5886 ------------------------------------------------------------------------------- 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: 0.7761 moved from start: 0.2022 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= 0.163 Angle : 0.397 4.620 5976 Z= 0.205 Chirality : 0.035 0.125 706 Planarity : 0.004 0.038 726 Dihedral : 8.140 59.876 628 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 22.10 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: 2.96 (0.38), residues: 541 helix: 2.78 (0.26), residues: 402 sheet: -2.52 (1.07), residues: 18 loop : -0.19 (0.62), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 34 HIS 0.002 0.001 HIS B 58 PHE 0.013 0.001 PHE A 312 TYR 0.006 0.001 TYR A 263 ARG 0.001 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 50 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.457 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 1.2266 time to fit residues: 63.9176 Evaluate side-chains 50 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.6683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.2078 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= 0.202 Angle : 0.425 4.717 5976 Z= 0.219 Chirality : 0.036 0.125 706 Planarity : 0.004 0.039 726 Dihedral : 7.809 56.285 628 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.53 % Allowed : 14.38 % 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: 2.83 (0.38), residues: 541 helix: 2.69 (0.26), residues: 402 sheet: -2.55 (1.08), residues: 18 loop : -0.31 (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 0.015 0.001 PHE A 312 TYR 0.007 0.001 TYR A 263 ARG 0.001 0.000 ARG A 236 ********************** 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 53 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.503 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 1.1945 time to fit residues: 63.5365 Evaluate side-chains 50 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0973 time to fit residues: 0.8023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.0570 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: 5.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.0370 chunk 31 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.166219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130815 restraints weight = 4665.477| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.68 r_work: 0.3460 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4419 Z= 0.156 Angle : 0.394 4.610 5976 Z= 0.204 Chirality : 0.035 0.125 706 Planarity : 0.004 0.039 726 Dihedral : 7.085 54.023 628 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: 2.98 (0.38), residues: 541 helix: 2.81 (0.27), residues: 402 sheet: -2.39 (1.11), residues: 18 loop : -0.28 (0.61), 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 0.015 0.001 PHE A 312 TYR 0.006 0.001 TYR A 263 ARG 0.001 0.000 ARG A 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1894.92 seconds wall clock time: 34 minutes 35.61 seconds (2075.61 seconds total)