Starting phenix.real_space_refine on Fri Apr 5 17:45:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2024/8bzy_16345_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2024/8bzy_16345.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2024/8bzy_16345_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2024/8bzy_16345_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2024/8bzy_16345_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2024/8bzy_16345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2024/8bzy_16345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2024/8bzy_16345_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2024/8bzy_16345_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 2817 2.51 5 N 702 2.21 5 O 759 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4311 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3300 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 9, 'TRANS': 419} Chain breaks: 2 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 942 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'PLC': 1, 'SZU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 3.02, per 1000 atoms: 0.70 Number of scatterers: 4311 At special positions: 0 Unit cell: (89.838, 87.885, 69.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 1 15.00 F 1 9.00 O 759 8.00 N 702 7.00 C 2817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 796.3 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: 1004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 3 sheets defined 68.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 19 through 22 Processing helix chain 'A' and resid 24 through 53 Processing helix chain 'A' and resid 58 through 85 removed outlier: 5.331A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 126 through 163 removed outlier: 4.025A pdb=" N THR A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 198 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 201 through 229 removed outlier: 3.730A pdb=" N VAL A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.647A pdb=" N ALA A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.855A pdb=" N TYR A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 339 through 366 removed outlier: 3.958A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 366 " --> pdb=" O TRP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 392 Processing helix chain 'A' and resid 452 through 483 removed outlier: 4.232A pdb=" N SER A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 513 removed outlier: 3.739A pdb=" N ARG A 489 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 545 removed outlier: 6.332A pdb=" N GLY A 521 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 4 through 7 Processing sheet with id= B, first strand: chain 'B' and resid 10 through 13 removed outlier: 4.187A pdb=" N GLU B 33 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA B 40 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ARG B 45 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 97 through 103 removed outlier: 5.791A pdb=" N TYR B 108 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY B 102 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 816 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: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 654 1.31 - 1.43: 1236 1.43 - 1.56: 2462 1.56 - 1.68: 2 1.68 - 1.81: 52 Bond restraints: 4406 Sorted by residual: bond pdb=" C3 SZU A 602 " pdb=" N2 SZU A 602 " ideal model delta sigma weight residual 1.376 1.321 0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" C4 PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 1.409 1.456 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C10 SZU A 602 " pdb=" C11 SZU A 602 " ideal model delta sigma weight residual 1.572 1.527 0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" C13 SZU A 602 " pdb=" C14 SZU A 602 " ideal model delta sigma weight residual 1.571 1.527 0.044 2.00e-02 2.50e+03 4.92e+00 bond pdb=" O4P PLC A 601 " pdb=" P PLC A 601 " ideal model delta sigma weight residual 1.648 1.605 0.043 2.00e-02 2.50e+03 4.63e+00 ... (remaining 4401 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 102 107.09 - 113.81: 2551 113.81 - 120.54: 1725 120.54 - 127.27: 1559 127.27 - 133.99: 51 Bond angle restraints: 5988 Sorted by residual: angle pdb=" C14 SZU A 602 " pdb=" C15 SZU A 602 " pdb=" N5 SZU A 602 " ideal model delta sigma weight residual 105.58 124.73 -19.15 3.00e+00 1.11e-01 4.07e+01 angle pdb=" C14 SZU A 602 " pdb=" C15 SZU A 602 " pdb=" N4 SZU A 602 " ideal model delta sigma weight residual 144.40 125.39 19.01 3.00e+00 1.11e-01 4.02e+01 angle pdb=" C11 SZU A 602 " pdb=" C10 SZU A 602 " pdb=" O2 SZU A 602 " ideal model delta sigma weight residual 110.79 125.10 -14.31 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C11 SZU A 602 " pdb=" C10 SZU A 602 " pdb=" N6 SZU A 602 " ideal model delta sigma weight residual 139.27 125.92 13.35 3.00e+00 1.11e-01 1.98e+01 angle pdb=" C6 SZU A 602 " pdb=" C7 SZU A 602 " pdb=" F1 SZU A 602 " ideal model delta sigma weight residual 107.80 120.40 -12.60 3.00e+00 1.11e-01 1.76e+01 ... (remaining 5983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.34: 2461 23.34 - 46.67: 71 46.67 - 70.01: 12 70.01 - 93.34: 0 93.34 - 116.68: 3 Dihedral angle restraints: 2547 sinusoidal: 973 harmonic: 1574 Sorted by residual: dihedral pdb=" C13 SZU A 602 " pdb=" C14 SZU A 602 " pdb=" C15 SZU A 602 " pdb=" N5 SZU A 602 " ideal model delta sinusoidal sigma weight residual 81.35 -35.33 116.68 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" O2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C2 PLC A 601 " pdb=" O3P PLC A 601 " ideal model delta sinusoidal sigma weight residual -55.71 54.64 -110.35 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" C3 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C2 PLC A 601 " pdb=" O3P PLC A 601 " ideal model delta sinusoidal sigma weight residual 67.16 177.18 -110.02 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 2544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 387 0.025 - 0.050: 193 0.050 - 0.075: 79 0.075 - 0.100: 29 0.100 - 0.125: 9 Chirality restraints: 697 Sorted by residual: chirality pdb=" CA VAL B 93 " pdb=" N VAL B 93 " pdb=" C VAL B 93 " pdb=" CB VAL B 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" C2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C3 PLC A 601 " pdb=" O2 PLC A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.44 0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA VAL B 79 " pdb=" N VAL B 79 " pdb=" C VAL B 79 " pdb=" CB VAL B 79 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.92e-01 ... (remaining 694 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 155 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C GLN A 155 " 0.033 2.00e-02 2.50e+03 pdb=" O GLN A 155 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 156 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 525 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C LEU A 525 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 525 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 526 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 527 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C SER A 527 " 0.028 2.00e-02 2.50e+03 pdb=" O SER A 527 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 528 " -0.009 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1238 2.82 - 3.34: 4411 3.34 - 3.86: 7367 3.86 - 4.38: 8166 4.38 - 4.90: 14663 Nonbonded interactions: 35845 Sorted by model distance: nonbonded pdb=" O ALA B 52 " pdb=" NH1 ARG B 72 " model vdw 2.297 2.520 nonbonded pdb=" OG SER A 390 " pdb=" O SER A 454 " model vdw 2.339 2.440 nonbonded pdb=" O ASN A 86 " pdb=" NZ LYS A 236 " model vdw 2.361 2.520 nonbonded pdb=" O VAL B 29 " pdb=" NH2 ARG B 72 " model vdw 2.398 2.520 nonbonded pdb=" O LEU A 60 " pdb=" OH TYR A 133 " model vdw 2.407 2.440 ... (remaining 35840 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.730 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.120 Find NCS groups from input model: 0.120 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 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 : 0.004 0.055 4406 Z= 0.263 Angle : 0.703 19.147 5988 Z= 0.310 Chirality : 0.037 0.125 697 Planarity : 0.004 0.026 725 Dihedral : 12.252 116.678 1540 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.42 % Allowed : 4.63 % Favored : 92.95 % 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: 2.10 (0.37), residues: 541 helix: 2.49 (0.27), residues: 366 sheet: 0.15 (0.76), residues: 40 loop : -1.43 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.002 0.001 HIS A 43 PHE 0.013 0.001 PHE A 295 TYR 0.008 0.001 TYR A 64 ARG 0.002 0.000 ARG A 178 *********************** 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 48 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.465 Fit side-chains REVERT: B 103 MET cc_start: 0.9205 (ptt) cc_final: 0.8682 (ptp) outliers start: 11 outliers final: 8 residues processed: 47 average time/residue: 0.1787 time to fit residues: 10.8751 Evaluate side-chains 45 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 228 GLN B 13 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4406 Z= 0.248 Angle : 0.485 8.535 5988 Z= 0.263 Chirality : 0.037 0.118 697 Planarity : 0.005 0.028 725 Dihedral : 10.698 118.141 646 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.30 % Allowed : 6.61 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.36), residues: 541 helix: 2.14 (0.26), residues: 366 sheet: -0.04 (0.74), residues: 40 loop : -1.36 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.003 0.001 HIS A 507 PHE 0.013 0.001 PHE A 295 TYR 0.015 0.001 TYR B 60 ARG 0.006 0.001 ARG B 19 *********************** 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 54 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.438 Fit side-chains REVERT: A 319 MET cc_start: 0.8479 (tpt) cc_final: 0.8208 (tpt) outliers start: 15 outliers final: 10 residues processed: 51 average time/residue: 0.1709 time to fit residues: 11.3287 Evaluate side-chains 48 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4406 Z= 0.250 Angle : 0.484 8.614 5988 Z= 0.259 Chirality : 0.037 0.119 697 Planarity : 0.004 0.026 725 Dihedral : 9.484 98.017 646 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.08 % Allowed : 7.71 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.36), residues: 541 helix: 1.99 (0.26), residues: 366 sheet: 0.42 (0.73), residues: 46 loop : -1.58 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.002 0.001 HIS A 507 PHE 0.012 0.001 PHE A 295 TYR 0.009 0.001 TYR B 60 ARG 0.006 0.000 ARG B 19 *********************** 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 52 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 38 time to evaluate : 0.456 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 50 average time/residue: 0.1638 time to fit residues: 10.7655 Evaluate side-chains 48 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 335 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4406 Z= 0.258 Angle : 0.479 8.697 5988 Z= 0.257 Chirality : 0.037 0.118 697 Planarity : 0.004 0.026 725 Dihedral : 9.058 90.814 645 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.96 % Allowed : 8.15 % Favored : 87.89 % 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: 1.50 (0.35), residues: 541 helix: 1.93 (0.26), residues: 367 sheet: 0.27 (0.73), residues: 46 loop : -1.54 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS A 507 PHE 0.012 0.001 PHE A 295 TYR 0.010 0.001 TYR A 227 ARG 0.007 0.001 ARG B 19 *********************** 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 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 38 time to evaluate : 0.454 Fit side-chains REVERT: B 38 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6858 (ptm160) REVERT: B 103 MET cc_start: 0.9190 (ptt) cc_final: 0.8945 (ptt) outliers start: 18 outliers final: 13 residues processed: 53 average time/residue: 0.1790 time to fit residues: 12.1016 Evaluate side-chains 52 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 38 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 0.0050 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4406 Z= 0.154 Angle : 0.426 6.998 5988 Z= 0.231 Chirality : 0.035 0.116 697 Planarity : 0.004 0.026 725 Dihedral : 8.541 85.745 645 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.30 % Allowed : 8.81 % Favored : 87.89 % 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: 1.80 (0.36), residues: 541 helix: 2.20 (0.26), residues: 366 sheet: 0.31 (0.73), residues: 46 loop : -1.52 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 106 HIS 0.002 0.001 HIS A 32 PHE 0.011 0.001 PHE A 295 TYR 0.019 0.001 TYR B 60 ARG 0.006 0.000 ARG B 19 *********************** 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 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.419 Fit side-chains REVERT: B 38 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6893 (ptm160) outliers start: 15 outliers final: 10 residues processed: 52 average time/residue: 0.1782 time to fit residues: 11.7866 Evaluate side-chains 50 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4406 Z= 0.247 Angle : 0.469 8.230 5988 Z= 0.254 Chirality : 0.036 0.117 697 Planarity : 0.004 0.026 725 Dihedral : 8.345 77.155 641 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.30 % Allowed : 8.81 % Favored : 87.89 % 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: 1.63 (0.35), residues: 541 helix: 2.04 (0.26), residues: 367 sheet: 0.22 (0.73), residues: 46 loop : -1.50 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 224 HIS 0.003 0.001 HIS A 507 PHE 0.012 0.001 PHE A 295 TYR 0.018 0.001 TYR B 60 ARG 0.008 0.001 ARG B 19 *********************** 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 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.452 Fit side-chains REVERT: B 38 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6883 (ptm160) REVERT: B 103 MET cc_start: 0.9075 (ptt) cc_final: 0.8765 (ptp) outliers start: 15 outliers final: 10 residues processed: 50 average time/residue: 0.1954 time to fit residues: 12.4774 Evaluate side-chains 50 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 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 228 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4406 Z= 0.226 Angle : 0.463 7.995 5988 Z= 0.251 Chirality : 0.036 0.117 697 Planarity : 0.004 0.026 725 Dihedral : 8.167 71.846 639 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.30 % Allowed : 9.25 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.35), residues: 541 helix: 2.05 (0.26), residues: 367 sheet: 0.24 (0.73), residues: 46 loop : -1.47 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 224 HIS 0.002 0.001 HIS A 507 PHE 0.012 0.001 PHE A 295 TYR 0.018 0.001 TYR B 60 ARG 0.008 0.001 ARG B 19 *********************** 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 53 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.463 Fit side-chains REVERT: A 111 MET cc_start: 0.6328 (ttm) cc_final: 0.6122 (ttm) REVERT: B 38 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6894 (ptm160) REVERT: B 103 MET cc_start: 0.9108 (ptt) cc_final: 0.8800 (ptp) outliers start: 15 outliers final: 11 residues processed: 50 average time/residue: 0.1808 time to fit residues: 11.5437 Evaluate side-chains 50 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 0.0040 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4406 Z= 0.197 Angle : 0.450 7.844 5988 Z= 0.245 Chirality : 0.036 0.117 697 Planarity : 0.004 0.026 725 Dihedral : 8.028 66.695 639 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.08 % Allowed : 9.47 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.36), residues: 541 helix: 2.14 (0.26), residues: 366 sheet: 0.31 (0.73), residues: 46 loop : -1.51 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 224 HIS 0.002 0.001 HIS A 32 PHE 0.011 0.001 PHE A 295 TYR 0.019 0.001 TYR B 60 ARG 0.009 0.001 ARG B 19 *********************** 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 52 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 38 time to evaluate : 0.446 Fit side-chains REVERT: A 111 MET cc_start: 0.6359 (ttm) cc_final: 0.6155 (ttm) REVERT: B 38 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6878 (ptm160) REVERT: B 103 MET cc_start: 0.9092 (ptt) cc_final: 0.8799 (ptp) outliers start: 14 outliers final: 11 residues processed: 50 average time/residue: 0.1855 time to fit residues: 11.7568 Evaluate side-chains 50 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4406 Z= 0.241 Angle : 0.474 8.369 5988 Z= 0.256 Chirality : 0.036 0.117 697 Planarity : 0.004 0.026 725 Dihedral : 8.056 62.036 639 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.30 % Allowed : 9.47 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.35), residues: 541 helix: 2.03 (0.26), residues: 367 sheet: 0.29 (0.73), residues: 46 loop : -1.46 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 224 HIS 0.003 0.001 HIS A 507 PHE 0.012 0.001 PHE A 295 TYR 0.017 0.001 TYR B 60 ARG 0.009 0.001 ARG B 19 *********************** 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 54 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.370 Fit side-chains REVERT: A 111 MET cc_start: 0.6378 (ttm) cc_final: 0.6143 (ttm) REVERT: B 38 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6879 (ptm160) REVERT: B 103 MET cc_start: 0.9098 (ptt) cc_final: 0.8769 (ptp) outliers start: 15 outliers final: 13 residues processed: 51 average time/residue: 0.1860 time to fit residues: 12.0060 Evaluate side-chains 53 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4406 Z= 0.214 Angle : 0.468 9.683 5988 Z= 0.251 Chirality : 0.036 0.117 697 Planarity : 0.004 0.028 725 Dihedral : 7.979 59.094 639 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.08 % Allowed : 9.69 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.35), residues: 541 helix: 2.08 (0.26), residues: 367 sheet: 0.32 (0.73), residues: 46 loop : -1.43 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 224 HIS 0.002 0.001 HIS A 507 PHE 0.011 0.001 PHE A 295 TYR 0.018 0.001 TYR B 60 ARG 0.009 0.001 ARG B 19 ********************** 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 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.478 Fit side-chains REVERT: A 111 MET cc_start: 0.6359 (ttm) cc_final: 0.6129 (ttm) REVERT: B 38 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6878 (ptm160) REVERT: B 103 MET cc_start: 0.9069 (ptt) cc_final: 0.8751 (ptp) outliers start: 14 outliers final: 12 residues processed: 50 average time/residue: 0.1912 time to fit residues: 12.2264 Evaluate side-chains 52 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.132139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.101250 restraints weight = 4562.729| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.82 r_work: 0.2919 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4406 Z= 0.210 Angle : 0.464 9.367 5988 Z= 0.250 Chirality : 0.036 0.117 697 Planarity : 0.004 0.026 725 Dihedral : 7.921 57.609 639 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.30 % Allowed : 9.69 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.35), residues: 541 helix: 2.12 (0.26), residues: 366 sheet: 0.31 (0.73), residues: 46 loop : -1.47 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 224 HIS 0.002 0.001 HIS A 32 PHE 0.011 0.001 PHE A 295 TYR 0.018 0.001 TYR B 60 ARG 0.009 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1386.84 seconds wall clock time: 25 minutes 42.64 seconds (1542.64 seconds total)