Starting phenix.real_space_refine on Fri Jul 19 04:30:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm4_17757/07_2024/8pm4_17757.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm4_17757/07_2024/8pm4_17757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm4_17757/07_2024/8pm4_17757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm4_17757/07_2024/8pm4_17757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm4_17757/07_2024/8pm4_17757.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm4_17757/07_2024/8pm4_17757.cif" } resolution = 2.93 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= 1.000 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 95 5.49 5 S 12 5.16 5 C 3790 2.51 5 N 1276 2.21 5 O 1451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6624 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4611 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 575} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1112 Classifications: {'RNA': 52} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 23, 'rna3p_pyr': 22} Link IDs: {'rna2p': 6, 'rna3p': 45} Chain: "C" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 558 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 343 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Time building chain proxies: 4.67, per 1000 atoms: 0.71 Number of scatterers: 6624 At special positions: 0 Unit cell: (99, 90.2, 101.2, 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 12 16.00 P 95 15.00 O 1451 8.00 N 1276 7.00 C 3790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 580 " 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: 3.25 Conformation dependent library (CDL) restraints added in 806.3 milliseconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1148 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 56.8% alpha, 14.2% beta 34 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 18 through 53 removed outlier: 3.593A pdb=" N ALA A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 84 Processing helix chain 'A' and resid 91 through 119 removed outlier: 4.112A pdb=" N ALA A 95 " --> pdb=" O HIS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 175 Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.935A pdb=" N THR A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 368 through 404 removed outlier: 4.020A pdb=" N GLU A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 425 through 439 removed outlier: 4.208A pdb=" N PHE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 491 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 588 through 604 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 5.704A pdb=" N ILE A 283 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS A 306 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 285 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ALA A 299 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 3 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR A 263 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER A 254 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU A 265 " --> pdb=" O CYS A 252 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 355 removed outlier: 3.673A pdb=" N ALA A 335 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 334 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 319 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASP A 497 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N VAL A 321 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 579 310 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1471 1.33 - 1.45: 1988 1.45 - 1.57: 3297 1.57 - 1.69: 188 1.69 - 1.81: 19 Bond restraints: 6963 Sorted by residual: bond pdb=" O4' DG C -9 " pdb=" C1' DG C -9 " ideal model delta sigma weight residual 1.414 1.384 0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" P DC D 0 " pdb=" OP2 DC D 0 " ideal model delta sigma weight residual 1.480 1.509 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" P DC D 0 " pdb=" OP1 DC D 0 " ideal model delta sigma weight residual 1.480 1.508 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" CG LEU A 288 " pdb=" CD1 LEU A 288 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 bond pdb=" CB ARG A 219 " pdb=" CG ARG A 219 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 ... (remaining 6958 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.23: 690 106.23 - 113.21: 3978 113.21 - 120.20: 2509 120.20 - 127.18: 2451 127.18 - 134.17: 285 Bond angle restraints: 9913 Sorted by residual: angle pdb=" N GLY A 148 " pdb=" CA GLY A 148 " pdb=" C GLY A 148 " ideal model delta sigma weight residual 113.18 119.98 -6.80 2.37e+00 1.78e-01 8.24e+00 angle pdb=" C2' G B 2 " pdb=" C1' G B 2 " pdb=" N9 G B 2 " ideal model delta sigma weight residual 112.00 115.70 -3.70 1.50e+00 4.44e-01 6.07e+00 angle pdb=" C2' A B 10 " pdb=" C1' A B 10 " pdb=" N9 A B 10 " ideal model delta sigma weight residual 112.00 115.33 -3.33 1.50e+00 4.44e-01 4.93e+00 angle pdb=" C4' DC D 0 " pdb=" O4' DC D 0 " pdb=" C1' DC D 0 " ideal model delta sigma weight residual 109.70 106.56 3.14 1.50e+00 4.44e-01 4.37e+00 angle pdb=" C ARG A 85 " pdb=" N THR A 86 " pdb=" CA THR A 86 " ideal model delta sigma weight residual 122.08 118.92 3.16 1.53e+00 4.27e-01 4.26e+00 ... (remaining 9908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.50: 3691 27.50 - 54.99: 354 54.99 - 82.49: 104 82.49 - 109.99: 1 109.99 - 137.49: 1 Dihedral angle restraints: 4151 sinusoidal: 2388 harmonic: 1763 Sorted by residual: dihedral pdb=" CA ARG A 88 " pdb=" C ARG A 88 " pdb=" N PRO A 89 " pdb=" CA PRO A 89 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CB CYS A 563 " pdb=" SG CYS A 563 " pdb=" SG CYS A 580 " pdb=" CB CYS A 580 " ideal model delta sinusoidal sigma weight residual -86.00 -118.48 32.48 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA ASP A 147 " pdb=" C ASP A 147 " pdb=" N GLY A 148 " pdb=" CA GLY A 148 " ideal model delta harmonic sigma weight residual 180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1062 0.074 - 0.147: 107 0.147 - 0.221: 1 0.221 - 0.294: 1 0.294 - 0.368: 1 Chirality restraints: 1172 Sorted by residual: chirality pdb=" P DC D 0 " pdb=" OP1 DC D 0 " pdb=" OP2 DC D 0 " pdb=" O5' DC D 0 " both_signs ideal model delta sigma weight residual True 2.35 -2.71 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" C1' G B 2 " pdb=" O4' G B 2 " pdb=" C2' G B 2 " pdb=" N9 G B 2 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C1' A B 10 " pdb=" O4' A B 10 " pdb=" C2' A B 10 " pdb=" N9 A B 10 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 1169 not shown) Planarity restraints: 929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 10 " -0.031 2.00e-02 2.50e+03 1.32e-02 4.79e+00 pdb=" N9 A B 10 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A B 10 " 0.007 2.00e-02 2.50e+03 pdb=" N7 A B 10 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A B 10 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 10 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A B 10 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A B 10 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A B 10 " 0.005 2.00e-02 2.50e+03 pdb=" N3 A B 10 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A B 10 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 4 " 0.028 2.00e-02 2.50e+03 1.37e-02 4.22e+00 pdb=" N1 U B 4 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U B 4 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U B 4 " -0.007 2.00e-02 2.50e+03 pdb=" N3 U B 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U B 4 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U B 4 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U B 4 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 4 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 2 " 0.029 2.00e-02 2.50e+03 1.17e-02 4.12e+00 pdb=" N9 G B 2 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B 2 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G B 2 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G B 2 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 2 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G B 2 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G B 2 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G B 2 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G B 2 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 2 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G B 2 " -0.004 2.00e-02 2.50e+03 ... (remaining 926 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1088 2.76 - 3.29: 6209 3.29 - 3.83: 12435 3.83 - 4.36: 14656 4.36 - 4.90: 22918 Nonbonded interactions: 57306 Sorted by model distance: nonbonded pdb=" NH1 ARG A 241 " pdb=" OP2 C B -5 " model vdw 2.220 2.520 nonbonded pdb=" NZ LYS A 460 " pdb=" OE2 GLU A 464 " model vdw 2.253 2.520 nonbonded pdb=" NH2 ARG A 393 " pdb=" O TRP A 423 " model vdw 2.254 2.520 nonbonded pdb=" OE2 GLU A 452 " pdb=" NH2 ARG A 455 " model vdw 2.264 2.520 nonbonded pdb=" NH2 ARG A 173 " pdb=" O ALA A 179 " model vdw 2.268 2.520 ... (remaining 57301 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: 0.600 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.180 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.007 0.045 6963 Z= 0.457 Angle : 0.634 6.801 9913 Z= 0.352 Chirality : 0.044 0.368 1172 Planarity : 0.006 0.046 929 Dihedral : 20.606 137.486 3000 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.32 % Allowed : 9.45 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.17 (0.33), residues: 602 helix: 1.89 (0.28), residues: 321 sheet: -0.65 (0.51), residues: 89 loop : -0.33 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 226 HIS 0.003 0.001 HIS A 183 PHE 0.007 0.002 PHE A 487 TYR 0.012 0.002 TYR A 42 ARG 0.004 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6596 (mp) outliers start: 6 outliers final: 0 residues processed: 56 average time/residue: 1.0268 time to fit residues: 61.3369 Evaluate side-chains 39 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7866 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6963 Z= 0.189 Angle : 0.503 5.578 9913 Z= 0.280 Chirality : 0.036 0.191 1172 Planarity : 0.004 0.036 929 Dihedral : 22.251 141.318 1979 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.30 % Allowed : 11.65 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.93 (0.34), residues: 602 helix: 2.47 (0.27), residues: 322 sheet: -0.24 (0.55), residues: 85 loop : -0.00 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 454 HIS 0.007 0.001 HIS A 565 PHE 0.005 0.001 PHE A 155 TYR 0.021 0.001 TYR A 587 ARG 0.005 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 276 MET cc_start: 0.9156 (mmt) cc_final: 0.8917 (mmt) REVERT: A 400 LEU cc_start: 0.7107 (mp) cc_final: 0.6648 (mp) REVERT: A 560 HIS cc_start: 0.7588 (t-170) cc_final: 0.7225 (t70) outliers start: 15 outliers final: 3 residues processed: 52 average time/residue: 1.0273 time to fit residues: 57.2055 Evaluate side-chains 44 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.7924 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 6963 Z= 0.371 Angle : 0.567 5.772 9913 Z= 0.313 Chirality : 0.040 0.205 1172 Planarity : 0.005 0.035 929 Dihedral : 22.156 139.366 1977 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.86 % Allowed : 13.85 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.34), residues: 602 helix: 2.24 (0.27), residues: 322 sheet: -0.25 (0.53), residues: 86 loop : 0.04 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 454 HIS 0.008 0.001 HIS A 565 PHE 0.006 0.002 PHE A 487 TYR 0.021 0.002 TYR A 587 ARG 0.006 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6734 (mp) REVERT: A 494 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8139 (tt) outliers start: 13 outliers final: 4 residues processed: 51 average time/residue: 1.0174 time to fit residues: 55.5890 Evaluate side-chains 47 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 494 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 54 optimal weight: 0.0000 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 2.1590 ------------------------------------------------------------------------------- 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: 0.7918 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6963 Z= 0.335 Angle : 0.552 5.730 9913 Z= 0.305 Chirality : 0.039 0.201 1172 Planarity : 0.005 0.036 929 Dihedral : 22.152 139.958 1977 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.08 % Allowed : 16.26 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.34), residues: 602 helix: 2.20 (0.27), residues: 322 sheet: -0.04 (0.57), residues: 76 loop : -0.08 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 454 HIS 0.009 0.001 HIS A 565 PHE 0.005 0.002 PHE A 155 TYR 0.026 0.002 TYR A 587 ARG 0.006 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7872 (tp40) REVERT: A 276 MET cc_start: 0.9118 (mmt) cc_final: 0.8895 (mmt) REVERT: A 400 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6726 (mp) outliers start: 14 outliers final: 5 residues processed: 50 average time/residue: 1.0854 time to fit residues: 58.4699 Evaluate side-chains 48 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 400 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 45 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.0470 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6963 Z= 0.154 Angle : 0.476 4.934 9913 Z= 0.265 Chirality : 0.034 0.170 1172 Planarity : 0.004 0.035 929 Dihedral : 22.029 139.681 1977 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.20 % Allowed : 17.36 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.31 (0.34), residues: 602 helix: 2.70 (0.28), residues: 322 sheet: 0.46 (0.59), residues: 75 loop : 0.06 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 454 HIS 0.010 0.001 HIS A 565 PHE 0.005 0.001 PHE A 155 TYR 0.025 0.001 TYR A 587 ARG 0.007 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7897 (tp40) REVERT: A 85 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6732 (mpp80) REVERT: A 141 TYR cc_start: 0.8369 (t80) cc_final: 0.7984 (t80) REVERT: A 235 MET cc_start: 0.9054 (ptm) cc_final: 0.8785 (ptm) REVERT: A 276 MET cc_start: 0.9110 (mmt) cc_final: 0.8843 (mmt) REVERT: A 560 HIS cc_start: 0.7666 (t-170) cc_final: 0.7023 (t-170) outliers start: 10 outliers final: 2 residues processed: 51 average time/residue: 1.0462 time to fit residues: 56.9544 Evaluate side-chains 48 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 556 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7870 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6963 Z= 0.227 Angle : 0.493 4.766 9913 Z= 0.273 Chirality : 0.036 0.181 1172 Planarity : 0.004 0.034 929 Dihedral : 21.946 137.927 1977 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.20 % Allowed : 16.48 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.24 (0.34), residues: 602 helix: 2.64 (0.28), residues: 322 sheet: 0.42 (0.58), residues: 75 loop : 0.06 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 454 HIS 0.010 0.001 HIS A 565 PHE 0.005 0.001 PHE A 155 TYR 0.023 0.002 TYR A 587 ARG 0.008 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 235 MET cc_start: 0.9050 (ptm) cc_final: 0.8736 (ptm) REVERT: A 276 MET cc_start: 0.9085 (mmt) cc_final: 0.8846 (mmt) outliers start: 10 outliers final: 3 residues processed: 49 average time/residue: 0.9805 time to fit residues: 51.5067 Evaluate side-chains 44 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.7959 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 6963 Z= 0.533 Angle : 0.645 6.044 9913 Z= 0.351 Chirality : 0.045 0.222 1172 Planarity : 0.005 0.040 929 Dihedral : 22.078 137.840 1977 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.54 % Allowed : 17.80 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.46 (0.34), residues: 602 helix: 1.90 (0.28), residues: 322 sheet: -0.07 (0.57), residues: 76 loop : -0.03 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 226 HIS 0.010 0.001 HIS A 565 PHE 0.010 0.003 PHE A 487 TYR 0.033 0.003 TYR A 587 ARG 0.007 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 235 MET cc_start: 0.9006 (ptm) cc_final: 0.8710 (ptm) REVERT: A 330 HIS cc_start: 0.8066 (m-70) cc_final: 0.7847 (m-70) REVERT: A 600 ARG cc_start: 0.7339 (mtm-85) cc_final: 0.7119 (ttp-170) outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 1.0686 time to fit residues: 53.7963 Evaluate side-chains 42 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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: 0.7937 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6963 Z= 0.394 Angle : 0.585 5.794 9913 Z= 0.320 Chirality : 0.041 0.213 1172 Planarity : 0.005 0.042 929 Dihedral : 22.094 139.418 1977 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.42 % Allowed : 17.80 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.48 (0.34), residues: 602 helix: 1.95 (0.28), residues: 322 sheet: -0.13 (0.58), residues: 76 loop : -0.05 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 454 HIS 0.011 0.001 HIS A 565 PHE 0.006 0.002 PHE A 487 TYR 0.030 0.002 TYR A 587 ARG 0.006 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 235 MET cc_start: 0.8997 (ptm) cc_final: 0.8731 (ptm) REVERT: A 276 MET cc_start: 0.9158 (mmt) cc_final: 0.8936 (mmt) REVERT: A 301 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8397 (mt) REVERT: A 330 HIS cc_start: 0.8043 (m-70) cc_final: 0.7790 (m-70) outliers start: 11 outliers final: 4 residues processed: 46 average time/residue: 1.1041 time to fit residues: 54.1509 Evaluate side-chains 43 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 400 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6963 Z= 0.228 Angle : 0.522 5.780 9913 Z= 0.288 Chirality : 0.037 0.189 1172 Planarity : 0.004 0.036 929 Dihedral : 22.039 139.626 1977 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.98 % Allowed : 18.90 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.87 (0.34), residues: 602 helix: 2.28 (0.28), residues: 322 sheet: 0.15 (0.60), residues: 75 loop : 0.05 (0.45), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 454 HIS 0.012 0.001 HIS A 565 PHE 0.005 0.002 PHE A 155 TYR 0.027 0.002 TYR A 587 ARG 0.006 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7695 (mm) cc_final: 0.7478 (mm) REVERT: A 85 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6364 (mtm-85) REVERT: A 141 TYR cc_start: 0.8436 (t80) cc_final: 0.7989 (t80) REVERT: A 235 MET cc_start: 0.9014 (ptm) cc_final: 0.8745 (ptm) REVERT: A 330 HIS cc_start: 0.7993 (m-70) cc_final: 0.7718 (m-70) outliers start: 9 outliers final: 3 residues processed: 53 average time/residue: 1.0681 time to fit residues: 60.3145 Evaluate side-chains 45 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 556 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.2980 chunk 7 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6963 Z= 0.171 Angle : 0.489 4.910 9913 Z= 0.270 Chirality : 0.035 0.171 1172 Planarity : 0.004 0.034 929 Dihedral : 21.943 138.572 1977 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.32 % Allowed : 19.56 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.17 (0.35), residues: 602 helix: 2.58 (0.28), residues: 322 sheet: 0.18 (0.57), residues: 83 loop : 0.12 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 454 HIS 0.013 0.001 HIS A 565 PHE 0.006 0.001 PHE A 487 TYR 0.029 0.002 TYR A 486 ARG 0.008 0.000 ARG A 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7737 (mm) cc_final: 0.7530 (mm) REVERT: A 85 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6066 (mtm-85) REVERT: A 235 MET cc_start: 0.9033 (ptm) cc_final: 0.8687 (ptm) outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 1.1073 time to fit residues: 62.4614 Evaluate side-chains 49 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 397 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.152712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119171 restraints weight = 8108.400| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.53 r_work: 0.3433 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6963 Z= 0.207 Angle : 0.500 4.727 9913 Z= 0.275 Chirality : 0.036 0.177 1172 Planarity : 0.004 0.034 929 Dihedral : 21.897 137.364 1977 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.54 % Allowed : 19.78 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.14 (0.35), residues: 602 helix: 2.56 (0.28), residues: 322 sheet: 0.22 (0.57), residues: 83 loop : 0.08 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 454 HIS 0.011 0.001 HIS A 565 PHE 0.005 0.001 PHE A 155 TYR 0.036 0.003 TYR A 486 ARG 0.004 0.000 ARG A 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1976.52 seconds wall clock time: 35 minutes 49.57 seconds (2149.57 seconds total)