Starting phenix.real_space_refine on Wed Oct 9 18:07:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1j_44081/10_2024/9b1j_44081.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1j_44081/10_2024/9b1j_44081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1j_44081/10_2024/9b1j_44081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1j_44081/10_2024/9b1j_44081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1j_44081/10_2024/9b1j_44081.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1j_44081/10_2024/9b1j_44081.cif" } resolution = 3.0 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= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 30 5.16 5 C 2570 2.51 5 N 666 2.21 5 O 686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 3953 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3922 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'NAG': 1, 'PO4': 1, 'URC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.80, per 1000 atoms: 0.96 Number of scatterers: 3953 At special positions: 0 Unit cell: (57.761, 90.211, 99.946, 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 30 16.00 P 1 15.00 O 686 8.00 N 666 7.00 C 2570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 56 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 641.7 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 950 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 81.9% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.732A pdb=" N TRP A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.745A pdb=" N GLY A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.536A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 221 removed outlier: 3.560A pdb=" N ALA A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 removed outlier: 6.174A pdb=" N ARG A 225 " --> pdb=" O THR A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 226 through 252 removed outlier: 4.277A pdb=" N PHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 264 through 274 removed outlier: 4.102A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.603A pdb=" N GLN A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.975A pdb=" N ALA A 308 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.882A pdb=" N VAL A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 removed outlier: 4.173A pdb=" N PHE A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 364 removed outlier: 4.642A pdb=" N PHE A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 356 " --> pdb=" O CYS A 352 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A 357 " --> pdb=" O TRP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 400 through 422 removed outlier: 4.053A pdb=" N THR A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 452 removed outlier: 3.695A pdb=" N THR A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 483 through 489 removed outlier: 4.042A pdb=" N VAL A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 4.145A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Proline residue: A 501 - end of helix removed outlier: 3.699A pdb=" N LEU A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 268 hydrogen bonds defined for protein. 768 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: 1.34 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1241 1.34 - 1.46: 920 1.46 - 1.58: 1844 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4052 Sorted by residual: bond pdb=" C2 URC A 602 " pdb=" O11 URC A 602 " ideal model delta sigma weight residual 1.213 1.364 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" C8 URC A 602 " pdb=" O24 URC A 602 " ideal model delta sigma weight residual 1.215 1.353 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C4 URC A 602 " pdb=" C5 URC A 602 " ideal model delta sigma weight residual 1.358 1.495 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" C6 URC A 602 " pdb=" O13 URC A 602 " ideal model delta sigma weight residual 1.218 1.348 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C8 URC A 602 " pdb=" N7 URC A 602 " ideal model delta sigma weight residual 1.360 1.435 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 4047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 5453 2.71 - 5.42: 61 5.42 - 8.13: 8 8.13 - 10.84: 4 10.84 - 13.55: 3 Bond angle restraints: 5529 Sorted by residual: angle pdb=" N1 URC A 602 " pdb=" C2 URC A 602 " pdb=" N3 URC A 602 " ideal model delta sigma weight residual 114.62 128.17 -13.55 3.00e+00 1.11e-01 2.04e+01 angle pdb=" N7 URC A 602 " pdb=" C8 URC A 602 " pdb=" N9 URC A 602 " ideal model delta sigma weight residual 104.73 116.67 -11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C2 URC A 602 " pdb=" N1 URC A 602 " pdb=" C6 URC A 602 " ideal model delta sigma weight residual 129.31 117.54 11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA ARG A 473 " pdb=" CB ARG A 473 " pdb=" CG ARG A 473 " ideal model delta sigma weight residual 114.10 107.00 7.10 2.00e+00 2.50e-01 1.26e+01 angle pdb=" C5 URC A 602 " pdb=" C6 URC A 602 " pdb=" N1 URC A 602 " ideal model delta sigma weight residual 111.19 121.50 -10.31 3.00e+00 1.11e-01 1.18e+01 ... (remaining 5524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 2229 16.05 - 32.11: 131 32.11 - 48.16: 21 48.16 - 64.22: 7 64.22 - 80.27: 3 Dihedral angle restraints: 2391 sinusoidal: 919 harmonic: 1472 Sorted by residual: dihedral pdb=" CA GLU A 38 " pdb=" C GLU A 38 " pdb=" N ASN A 39 " pdb=" CA ASN A 39 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PHE A 361 " pdb=" C PHE A 361 " pdb=" N GLY A 362 " pdb=" CA GLY A 362 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PRO A 457 " pdb=" C PRO A 457 " pdb=" N THR A 458 " pdb=" CA THR A 458 " ideal model delta harmonic sigma weight residual -180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 356 0.026 - 0.051: 176 0.051 - 0.077: 74 0.077 - 0.103: 31 0.103 - 0.128: 14 Chirality restraints: 651 Sorted by residual: chirality pdb=" CA PRO A 52 " pdb=" N PRO A 52 " pdb=" C PRO A 52 " pdb=" CB PRO A 52 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA PRO A 501 " pdb=" N PRO A 501 " pdb=" C PRO A 501 " pdb=" CB PRO A 501 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA TYR A 272 " pdb=" N TYR A 272 " pdb=" C TYR A 272 " pdb=" CB TYR A 272 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 648 not shown) Planarity restraints: 686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 358 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C PHE A 358 " -0.027 2.00e-02 2.50e+03 pdb=" O PHE A 358 " 0.010 2.00e-02 2.50e+03 pdb=" N THR A 359 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 297 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C ARG A 297 " 0.026 2.00e-02 2.50e+03 pdb=" O ARG A 297 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 298 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 483 " -0.116 9.50e-02 1.11e+02 5.18e-02 1.65e+00 pdb=" NE ARG A 483 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 483 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 483 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 483 " -0.004 2.00e-02 2.50e+03 ... (remaining 683 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1557 2.89 - 3.39: 3985 3.39 - 3.90: 6535 3.90 - 4.40: 7587 4.40 - 4.90: 12585 Nonbonded interactions: 32249 Sorted by model distance: nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.389 3.040 nonbonded pdb=" OG SER A 239 " pdb=" OD2 ASP A 385 " model vdw 2.409 3.040 nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.450 3.040 nonbonded pdb=" NE ARG A 473 " pdb=" O3 PO4 A 603 " model vdw 2.467 3.120 nonbonded pdb=" OD1 ASN A 56 " pdb=" OG1 THR A 58 " model vdw 2.494 3.040 ... (remaining 32244 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.380 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.006 0.151 4052 Z= 0.411 Angle : 0.833 13.548 5529 Z= 0.409 Chirality : 0.040 0.128 651 Planarity : 0.005 0.052 685 Dihedral : 11.220 80.271 1435 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.36), residues: 513 helix: 0.01 (0.26), residues: 358 sheet: -1.68 (1.59), residues: 10 loop : 1.41 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 50 HIS 0.004 0.001 HIS A 398 PHE 0.015 0.002 PHE A 356 TYR 0.020 0.002 TYR A 272 ARG 0.004 0.001 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.415 Fit side-chains REVERT: A 115 ASP cc_start: 0.8474 (m-30) cc_final: 0.8099 (m-30) REVERT: A 126 SER cc_start: 0.8831 (t) cc_final: 0.8425 (m) REVERT: A 144 MET cc_start: 0.7503 (ttm) cc_final: 0.7286 (ttt) REVERT: A 225 ARG cc_start: 0.6953 (ptt180) cc_final: 0.6463 (ptp-170) REVERT: A 285 ILE cc_start: 0.7800 (mt) cc_final: 0.7474 (mp) REVERT: A 295 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6880 (mm-30) REVERT: A 390 MET cc_start: 0.7370 (mmm) cc_final: 0.7162 (mmp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 1.0556 time to fit residues: 67.3807 Evaluate side-chains 53 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4052 Z= 0.209 Angle : 0.577 6.416 5529 Z= 0.295 Chirality : 0.041 0.124 651 Planarity : 0.005 0.041 685 Dihedral : 4.291 16.272 569 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.44 % Allowed : 7.93 % Favored : 90.62 % 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: 1.51 (0.37), residues: 513 helix: 0.93 (0.27), residues: 354 sheet: None (None), residues: 0 loop : 1.57 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 50 HIS 0.004 0.001 HIS A 139 PHE 0.014 0.002 PHE A 354 TYR 0.019 0.002 TYR A 272 ARG 0.003 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.491 Fit side-chains REVERT: A 115 ASP cc_start: 0.8336 (m-30) cc_final: 0.8116 (m-30) REVERT: A 126 SER cc_start: 0.8852 (t) cc_final: 0.8383 (m) REVERT: A 225 ARG cc_start: 0.7033 (ptt180) cc_final: 0.6482 (ptp-170) REVERT: A 285 ILE cc_start: 0.7835 (mt) cc_final: 0.7501 (mt) REVERT: A 295 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6963 (mm-30) outliers start: 6 outliers final: 2 residues processed: 55 average time/residue: 0.9621 time to fit residues: 55.9356 Evaluate side-chains 48 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 272 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4052 Z= 0.273 Angle : 0.609 6.668 5529 Z= 0.306 Chirality : 0.042 0.121 651 Planarity : 0.005 0.041 685 Dihedral : 4.054 14.749 569 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.12 % Allowed : 8.89 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.37), residues: 513 helix: 0.87 (0.27), residues: 358 sheet: -2.06 (1.66), residues: 10 loop : 0.96 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 50 HIS 0.004 0.001 HIS A 83 PHE 0.017 0.002 PHE A 354 TYR 0.017 0.002 TYR A 272 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.467 Fit side-chains REVERT: A 126 SER cc_start: 0.8902 (t) cc_final: 0.8388 (m) REVERT: A 225 ARG cc_start: 0.7188 (ptt180) cc_final: 0.6642 (ptp-170) REVERT: A 285 ILE cc_start: 0.7782 (mt) cc_final: 0.7460 (mt) REVERT: A 401 ARG cc_start: 0.3765 (OUTLIER) cc_final: 0.3104 (mmt180) outliers start: 13 outliers final: 5 residues processed: 51 average time/residue: 0.9808 time to fit residues: 52.6181 Evaluate side-chains 48 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4052 Z= 0.187 Angle : 0.538 6.786 5529 Z= 0.269 Chirality : 0.039 0.118 651 Planarity : 0.004 0.038 685 Dihedral : 3.827 14.545 569 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.16 % Allowed : 9.86 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.37), residues: 513 helix: 1.06 (0.27), residues: 365 sheet: -2.78 (1.43), residues: 10 loop : 1.23 (0.57), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 175 HIS 0.003 0.001 HIS A 242 PHE 0.015 0.001 PHE A 354 TYR 0.016 0.002 TYR A 272 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.398 Fit side-chains REVERT: A 115 ASP cc_start: 0.8291 (m-30) cc_final: 0.8089 (m-30) REVERT: A 126 SER cc_start: 0.8859 (t) cc_final: 0.8354 (m) REVERT: A 225 ARG cc_start: 0.7156 (ptt180) cc_final: 0.6609 (ptp-170) REVERT: A 312 THR cc_start: 0.7045 (OUTLIER) cc_final: 0.6802 (t) REVERT: A 401 ARG cc_start: 0.3873 (OUTLIER) cc_final: 0.3166 (mmt180) REVERT: A 485 LEU cc_start: 0.7149 (mt) cc_final: 0.6945 (mt) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.8374 time to fit residues: 41.4129 Evaluate side-chains 45 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 20 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4052 Z= 0.171 Angle : 0.518 7.004 5529 Z= 0.257 Chirality : 0.039 0.119 651 Planarity : 0.004 0.036 685 Dihedral : 3.644 13.569 569 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.37 % Allowed : 7.93 % Favored : 88.70 % 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: 1.97 (0.38), residues: 513 helix: 1.54 (0.27), residues: 350 sheet: -2.55 (1.57), residues: 10 loop : 1.35 (0.56), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 175 HIS 0.003 0.001 HIS A 242 PHE 0.014 0.001 PHE A 354 TYR 0.022 0.003 TYR A 272 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.375 Fit side-chains REVERT: A 36 MET cc_start: 0.8077 (mmt) cc_final: 0.7875 (mmm) REVERT: A 126 SER cc_start: 0.8851 (t) cc_final: 0.8338 (m) REVERT: A 219 MET cc_start: 0.7036 (mtp) cc_final: 0.6786 (mtp) REVERT: A 225 ARG cc_start: 0.7161 (ptt180) cc_final: 0.6540 (ptp-170) REVERT: A 312 THR cc_start: 0.7019 (OUTLIER) cc_final: 0.6782 (t) REVERT: A 401 ARG cc_start: 0.3822 (OUTLIER) cc_final: 0.3191 (mmt180) REVERT: A 446 THR cc_start: 0.6724 (m) cc_final: 0.6337 (p) REVERT: A 485 LEU cc_start: 0.7056 (mt) cc_final: 0.6855 (mt) outliers start: 14 outliers final: 5 residues processed: 52 average time/residue: 0.9832 time to fit residues: 53.7950 Evaluate side-chains 42 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4052 Z= 0.212 Angle : 0.542 7.168 5529 Z= 0.268 Chirality : 0.040 0.119 651 Planarity : 0.004 0.037 685 Dihedral : 3.663 13.440 569 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.16 % Allowed : 10.58 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.38), residues: 513 helix: 1.51 (0.27), residues: 350 sheet: -2.55 (1.70), residues: 10 loop : 1.38 (0.56), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.003 0.001 HIS A 139 PHE 0.015 0.002 PHE A 354 TYR 0.018 0.002 TYR A 272 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.435 Fit side-chains REVERT: A 126 SER cc_start: 0.8849 (t) cc_final: 0.8337 (m) REVERT: A 219 MET cc_start: 0.7083 (mtp) cc_final: 0.6819 (mtp) REVERT: A 225 ARG cc_start: 0.7150 (ptt180) cc_final: 0.6542 (ptp-170) REVERT: A 401 ARG cc_start: 0.3805 (OUTLIER) cc_final: 0.3149 (mmt180) REVERT: A 485 LEU cc_start: 0.7101 (mt) cc_final: 0.6873 (mt) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 1.1154 time to fit residues: 50.1956 Evaluate side-chains 42 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.0670 chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 0.0870 chunk 33 optimal weight: 0.0570 overall best weight: 0.1014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4052 Z= 0.133 Angle : 0.489 7.081 5529 Z= 0.239 Chirality : 0.037 0.121 651 Planarity : 0.004 0.033 685 Dihedral : 3.447 12.795 569 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.20 % Allowed : 11.54 % Favored : 87.26 % 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: 2.46 (0.38), residues: 513 helix: 1.99 (0.28), residues: 346 sheet: -2.16 (1.82), residues: 10 loop : 1.31 (0.56), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.003 0.001 HIS A 242 PHE 0.010 0.001 PHE A 201 TYR 0.014 0.002 TYR A 497 ARG 0.002 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.386 Fit side-chains REVERT: A 219 MET cc_start: 0.6969 (mtp) cc_final: 0.6725 (mtp) REVERT: A 312 THR cc_start: 0.7008 (OUTLIER) cc_final: 0.6724 (t) REVERT: A 446 THR cc_start: 0.6607 (m) cc_final: 0.6237 (p) outliers start: 5 outliers final: 1 residues processed: 43 average time/residue: 0.9141 time to fit residues: 41.4837 Evaluate side-chains 35 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 42 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4052 Z= 0.160 Angle : 0.515 8.042 5529 Z= 0.250 Chirality : 0.038 0.119 651 Planarity : 0.004 0.034 685 Dihedral : 3.399 12.074 569 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.68 % Allowed : 12.02 % Favored : 86.30 % 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: 2.45 (0.38), residues: 513 helix: 1.95 (0.27), residues: 346 sheet: -2.23 (1.73), residues: 10 loop : 1.38 (0.56), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.003 0.001 HIS A 242 PHE 0.012 0.001 PHE A 354 TYR 0.021 0.002 TYR A 272 ARG 0.002 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.482 Fit side-chains REVERT: A 219 MET cc_start: 0.6956 (mtp) cc_final: 0.6710 (mtp) REVERT: A 401 ARG cc_start: 0.3894 (OUTLIER) cc_final: 0.3213 (mmt180) REVERT: A 446 THR cc_start: 0.6667 (m) cc_final: 0.6272 (p) outliers start: 7 outliers final: 2 residues processed: 40 average time/residue: 1.2326 time to fit residues: 51.7254 Evaluate side-chains 36 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.0020 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4052 Z= 0.204 Angle : 0.552 8.358 5529 Z= 0.269 Chirality : 0.040 0.131 651 Planarity : 0.004 0.035 685 Dihedral : 3.482 12.510 569 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.96 % Allowed : 13.22 % Favored : 85.82 % 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: 2.27 (0.38), residues: 513 helix: 1.75 (0.27), residues: 350 sheet: -2.33 (1.74), residues: 10 loop : 1.50 (0.57), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 175 HIS 0.003 0.001 HIS A 242 PHE 0.014 0.001 PHE A 354 TYR 0.020 0.002 TYR A 272 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.405 Fit side-chains REVERT: A 126 SER cc_start: 0.8895 (t) cc_final: 0.8390 (m) REVERT: A 219 MET cc_start: 0.7000 (mtp) cc_final: 0.6669 (mtp) REVERT: A 401 ARG cc_start: 0.3895 (OUTLIER) cc_final: 0.3150 (mmt180) REVERT: A 446 THR cc_start: 0.6697 (m) cc_final: 0.6297 (p) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.9152 time to fit residues: 39.7009 Evaluate side-chains 37 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.2980 chunk 31 optimal weight: 0.0570 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.0370 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4052 Z= 0.152 Angle : 0.524 8.637 5529 Z= 0.253 Chirality : 0.038 0.119 651 Planarity : 0.004 0.034 685 Dihedral : 3.437 12.520 569 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.72 % Allowed : 13.22 % 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: 2.45 (0.38), residues: 513 helix: 1.94 (0.27), residues: 346 sheet: -2.20 (1.71), residues: 10 loop : 1.42 (0.56), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 175 HIS 0.003 0.001 HIS A 242 PHE 0.011 0.001 PHE A 354 TYR 0.014 0.002 TYR A 272 ARG 0.002 0.000 ARG A 473 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.402 Fit side-chains REVERT: A 219 MET cc_start: 0.7007 (mtp) cc_final: 0.6752 (mtp) REVERT: A 401 ARG cc_start: 0.3965 (OUTLIER) cc_final: 0.3183 (mmt180) REVERT: A 446 THR cc_start: 0.6663 (m) cc_final: 0.6270 (p) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 1.1264 time to fit residues: 40.2135 Evaluate side-chains 34 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 401 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.195388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.150400 restraints weight = 4145.091| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.72 r_work: 0.3469 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4052 Z= 0.181 Angle : 0.545 9.463 5529 Z= 0.264 Chirality : 0.039 0.132 651 Planarity : 0.004 0.035 685 Dihedral : 3.449 12.429 569 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.96 % Allowed : 12.98 % 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: 2.41 (0.38), residues: 513 helix: 1.91 (0.27), residues: 344 sheet: -2.40 (1.68), residues: 10 loop : 1.42 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 175 HIS 0.004 0.001 HIS A 242 PHE 0.013 0.001 PHE A 354 TYR 0.023 0.002 TYR A 272 ARG 0.002 0.000 ARG A 473 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1832.15 seconds wall clock time: 40 minutes 35.63 seconds (2435.63 seconds total)