Starting phenix.real_space_refine on Thu Nov 14 22:15:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k66_36918/11_2024/8k66_36918.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k66_36918/11_2024/8k66_36918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k66_36918/11_2024/8k66_36918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k66_36918/11_2024/8k66_36918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k66_36918/11_2024/8k66_36918.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k66_36918/11_2024/8k66_36918.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 34 5.16 5 Na 4 4.78 5 C 5070 2.51 5 N 1120 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7620 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3514 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 443, 3511 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 443, 3511 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424} Chain breaks: 2 bond proxies already assigned to first conformer: 3595 Chain: "B" Number of atoms: 3514 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 443, 3511 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 443, 3511 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424} Chain breaks: 2 bond proxies already assigned to first conformer: 3595 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 231 Unusual residues: {' NA': 2, 'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 231 Unusual residues: {' NA': 2, 'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Time building chain proxies: 10.05, per 1000 atoms: 1.32 Number of scatterers: 7620 At special positions: 0 Unit cell: (104.498, 110.423, 82.4135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 6 15.00 Na 4 11.00 O 1386 8.00 N 1120 7.00 C 5070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG ACYS A 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG ACYS B 488 " distance=2.05 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 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.5 seconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 77.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 22 through 38 removed outlier: 3.803A pdb=" N PHE A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 62 Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 181 through 214 Processing helix chain 'A' and resid 214 through 225 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 227 through 241 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 258 through 273 Processing helix chain 'A' and resid 275 through 292 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.684A pdb=" N LYS A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.608A pdb=" N GLU A 305 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 340 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 378 through 391 removed outlier: 3.564A pdb=" N LEU A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 423 Processing helix chain 'A' and resid 425 through 441 Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.535A pdb=" N LEU A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 516 removed outlier: 3.552A pdb=" N LEU A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 39 through 62 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 181 through 214 Processing helix chain 'B' and resid 214 through 225 Proline residue: B 220 - end of helix Processing helix chain 'B' and resid 227 through 241 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 258 through 273 Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.599A pdb=" N LYS B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 340 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 349 through 364 Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 378 through 391 removed outlier: 3.535A pdb=" N LEU B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 423 Processing helix chain 'B' and resid 425 through 441 Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.533A pdb=" N LEU B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 500 through 516 removed outlier: 3.550A pdb=" N LEU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528 486 hydrogen bonds defined for protein. 1389 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: 2.23 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1052 1.31 - 1.44: 2090 1.44 - 1.57: 4466 1.57 - 1.71: 12 1.71 - 1.84: 58 Bond restraints: 7678 Sorted by residual: bond pdb=" CA SER A 87 " pdb=" CB SER A 87 " ideal model delta sigma weight residual 1.531 1.461 0.070 1.56e-02 4.11e+03 2.04e+01 bond pdb=" CA SER B 87 " pdb=" CB SER B 87 " ideal model delta sigma weight residual 1.531 1.462 0.070 1.56e-02 4.11e+03 1.99e+01 bond pdb=" C11 T7X B 704 " pdb=" O18 T7X B 704 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C11 T7X A 603 " pdb=" O18 T7X A 603 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" N ILE A 90 " pdb=" CA ILE A 90 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.14e-02 7.69e+03 1.16e+01 ... (remaining 7673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 10176 3.20 - 6.40: 208 6.40 - 9.60: 28 9.60 - 12.80: 2 12.80 - 15.99: 6 Bond angle restraints: 10420 Sorted by residual: angle pdb=" O1 T7X B 704 " pdb=" P1 T7X B 704 " pdb=" O13 T7X B 704 " ideal model delta sigma weight residual 94.60 110.59 -15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O1 T7X A 603 " pdb=" P1 T7X A 603 " pdb=" O13 T7X A 603 " ideal model delta sigma weight residual 94.60 110.57 -15.97 3.00e+00 1.11e-01 2.83e+01 angle pdb=" O11 PTY B 705 " pdb=" P1 PTY B 705 " pdb=" O14 PTY B 705 " ideal model delta sigma weight residual 92.90 108.67 -15.77 3.00e+00 1.11e-01 2.76e+01 angle pdb=" O11 PTY A 604 " pdb=" P1 PTY A 604 " pdb=" O14 PTY A 604 " ideal model delta sigma weight residual 92.90 108.64 -15.74 3.00e+00 1.11e-01 2.75e+01 angle pdb=" O12 PC1 B 701 " pdb=" P PC1 B 701 " pdb=" O14 PC1 B 701 " ideal model delta sigma weight residual 123.67 110.29 13.38 3.00e+00 1.11e-01 1.99e+01 ... (remaining 10415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.32: 4594 32.32 - 64.63: 248 64.63 - 96.95: 35 96.95 - 129.27: 11 129.27 - 161.58: 2 Dihedral angle restraints: 4890 sinusoidal: 2308 harmonic: 2582 Sorted by residual: dihedral pdb=" C9 T7X B 704 " pdb=" C7 T7X B 704 " pdb=" C8 T7X B 704 " pdb=" O13 T7X B 704 " ideal model delta sinusoidal sigma weight residual 64.16 -134.26 -161.58 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C9 T7X A 603 " pdb=" C7 T7X A 603 " pdb=" C8 T7X A 603 " pdb=" O13 T7X A 603 " ideal model delta sinusoidal sigma weight residual 64.16 -134.27 -161.57 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA ILE A 300 " pdb=" C ILE A 300 " pdb=" N LYS A 301 " pdb=" CA LYS A 301 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 4887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.957: 1226 0.957 - 1.914: 0 1.914 - 2.871: 0 2.871 - 3.827: 0 3.827 - 4.784: 2 Chirality restraints: 1228 Sorted by residual: chirality pdb=" C1 T7X B 704 " pdb=" C2 T7X B 704 " pdb=" C6 T7X B 704 " pdb=" O1 T7X B 704 " both_signs ideal model delta sigma weight residual False -2.42 2.37 -4.78 2.00e-01 2.50e+01 5.72e+02 chirality pdb=" C1 T7X A 603 " pdb=" C2 T7X A 603 " pdb=" C6 T7X A 603 " pdb=" O1 T7X A 603 " both_signs ideal model delta sigma weight residual False -2.42 2.36 -4.78 2.00e-01 2.50e+01 5.72e+02 chirality pdb=" CBG Y01 B 702 " pdb=" CAQ Y01 B 702 " pdb=" CBD Y01 B 702 " pdb=" CBI Y01 B 702 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1225 not shown) Planarity restraints: 1202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 249 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C ASN B 249 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN B 249 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU B 250 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 246 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO B 247 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 246 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 247 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " 0.021 5.00e-02 4.00e+02 ... (remaining 1199 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 85 2.58 - 3.16: 6031 3.16 - 3.74: 12201 3.74 - 4.32: 18197 4.32 - 4.90: 29062 Nonbonded interactions: 65576 Sorted by model distance: nonbonded pdb=" NH2 ARG A 478 " pdb=" O HOH A 701 " model vdw 1.997 3.120 nonbonded pdb=" O LEU A 245 " pdb=" O HOH A 702 " model vdw 2.011 3.040 nonbonded pdb=" O LEU B 86 " pdb="NA NA B 707 " model vdw 2.027 2.470 nonbonded pdb=" O HOH A 750 " pdb=" O HOH A 762 " model vdw 2.039 3.040 nonbonded pdb=" O HOH B 819 " pdb=" O HOH B 860 " model vdw 2.042 3.040 ... (remaining 65571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 487 or resid 489 through 530 or resid 602 or re \ sid 607 through 608)) selection = (chain 'B' and (resid 22 through 487 or resid 489 through 530 or resid 702 or re \ sid 707 through 708)) } 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=0.50 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: 7.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.730 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 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 0.073 7678 Z= 0.375 Angle : 1.049 15.995 10420 Z= 0.468 Chirality : 0.199 4.784 1228 Planarity : 0.004 0.045 1202 Dihedral : 19.607 161.581 3216 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.20 % Allowed : 13.68 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -0.42 (0.26), residues: 876 helix: 0.39 (0.19), residues: 626 sheet: None (None), residues: 0 loop : -1.86 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 285 HIS 0.002 0.001 HIS B 200 PHE 0.013 0.001 PHE B 196 TYR 0.015 0.002 TYR B 195 ARG 0.005 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.762 Fit side-chains REVERT: A 61 PHE cc_start: 0.7266 (m-10) cc_final: 0.6881 (m-80) REVERT: A 63 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7480 (mmpt) REVERT: A 185 ARG cc_start: 0.7666 (ttp-170) cc_final: 0.7234 (ttm-80) REVERT: A 304 GLU cc_start: 0.7311 (pm20) cc_final: 0.6992 (mp0) REVERT: A 414 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.6036 (tptp) REVERT: A 422 LEU cc_start: 0.8354 (tp) cc_final: 0.8146 (tp) REVERT: B 70 ARG cc_start: 0.6811 (mtm-85) cc_final: 0.6486 (mpp-170) REVERT: B 185 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7343 (ttm-80) REVERT: B 422 LEU cc_start: 0.8354 (tp) cc_final: 0.8137 (tp) outliers start: 25 outliers final: 9 residues processed: 141 average time/residue: 1.4749 time to fit residues: 217.8715 Evaluate side-chains 115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 415 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 39 HIS A 200 HIS A 273 ASN A 421 ASN A 483 HIS B 25 ASN B 31 HIS B 39 HIS B 200 HIS B 273 ASN B 421 ASN B 483 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7678 Z= 0.221 Angle : 0.576 6.735 10420 Z= 0.297 Chirality : 0.040 0.130 1228 Planarity : 0.005 0.041 1202 Dihedral : 15.007 157.189 1641 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.94 % Allowed : 14.58 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 1.29 (0.28), residues: 876 helix: 1.59 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -1.07 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 42 HIS 0.003 0.001 HIS A 483 PHE 0.013 0.001 PHE B 196 TYR 0.016 0.002 TYR B 195 ARG 0.006 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.825 Fit side-chains REVERT: A 61 PHE cc_start: 0.7210 (m-10) cc_final: 0.6857 (m-80) REVERT: A 68 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: A 185 ARG cc_start: 0.7711 (ttp-170) cc_final: 0.7263 (ttm-80) REVERT: A 213 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6535 (mmt180) REVERT: A 252 MET cc_start: 0.8776 (mmt) cc_final: 0.8502 (mmt) REVERT: A 304 GLU cc_start: 0.7343 (pm20) cc_final: 0.7067 (mp0) REVERT: A 529 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9108 (mp) REVERT: B 185 ARG cc_start: 0.7695 (ttp-170) cc_final: 0.7314 (ttm-80) REVERT: B 252 MET cc_start: 0.8748 (mmt) cc_final: 0.8503 (mmt) REVERT: B 422 LEU cc_start: 0.8378 (tp) cc_final: 0.8167 (tp) REVERT: B 529 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9115 (mp) outliers start: 21 outliers final: 13 residues processed: 120 average time/residue: 1.3333 time to fit residues: 169.1936 Evaluate side-chains 113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN B 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7678 Z= 0.175 Angle : 0.523 5.825 10420 Z= 0.272 Chirality : 0.038 0.127 1228 Planarity : 0.004 0.041 1202 Dihedral : 13.967 153.646 1626 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.81 % Allowed : 15.09 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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 (0.29), residues: 876 helix: 2.03 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.83 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 285 HIS 0.002 0.001 HIS A 39 PHE 0.013 0.001 PHE B 196 TYR 0.015 0.002 TYR A 195 ARG 0.009 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.767 Fit side-chains REVERT: A 61 PHE cc_start: 0.7129 (m-10) cc_final: 0.6682 (m-80) REVERT: A 68 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: A 70 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7192 (ptp90) REVERT: A 185 ARG cc_start: 0.7683 (ttp-170) cc_final: 0.7230 (ttm-80) REVERT: A 252 MET cc_start: 0.8780 (mmt) cc_final: 0.8568 (mmt) REVERT: A 304 GLU cc_start: 0.7378 (pm20) cc_final: 0.7086 (mp0) REVERT: A 478 ARG cc_start: 0.8170 (mtp180) cc_final: 0.7896 (mtm180) REVERT: A 529 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9121 (mp) REVERT: B 185 ARG cc_start: 0.7688 (ttp-170) cc_final: 0.7310 (ttm-80) REVERT: B 422 LEU cc_start: 0.8336 (tp) cc_final: 0.8130 (tp) REVERT: B 529 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9127 (mp) outliers start: 20 outliers final: 8 residues processed: 120 average time/residue: 1.3970 time to fit residues: 176.7483 Evaluate side-chains 113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN B 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7678 Z= 0.162 Angle : 0.511 6.119 10420 Z= 0.265 Chirality : 0.038 0.127 1228 Planarity : 0.004 0.040 1202 Dihedral : 13.381 149.582 1620 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.30 % Allowed : 15.60 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.19 (0.29), residues: 876 helix: 2.22 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.72 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 285 HIS 0.002 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.015 0.002 TYR B 195 ARG 0.010 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.926 Fit side-chains REVERT: A 61 PHE cc_start: 0.7086 (m-10) cc_final: 0.6572 (m-80) REVERT: A 68 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: A 70 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7166 (ptp90) REVERT: A 185 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7245 (ttm-80) REVERT: A 252 MET cc_start: 0.8789 (mmt) cc_final: 0.8569 (mmt) REVERT: A 304 GLU cc_start: 0.7341 (pm20) cc_final: 0.7045 (mp0) REVERT: A 478 ARG cc_start: 0.8175 (mtp180) cc_final: 0.7886 (mtm180) REVERT: A 529 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9115 (mp) REVERT: B 185 ARG cc_start: 0.7690 (ttp-170) cc_final: 0.7314 (ttm-80) REVERT: B 422 LEU cc_start: 0.8308 (tp) cc_final: 0.8107 (tp) REVERT: B 529 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9120 (mp) outliers start: 16 outliers final: 8 residues processed: 116 average time/residue: 1.3909 time to fit residues: 170.1525 Evaluate side-chains 114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.0020 chunk 1 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN B 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7678 Z= 0.139 Angle : 0.485 5.793 10420 Z= 0.252 Chirality : 0.037 0.120 1228 Planarity : 0.004 0.038 1202 Dihedral : 12.886 147.058 1620 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.17 % Allowed : 15.86 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.40 (0.29), residues: 876 helix: 2.39 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.70 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 285 HIS 0.001 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.014 0.002 TYR B 195 ARG 0.010 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.822 Fit side-chains REVERT: A 61 PHE cc_start: 0.6993 (m-10) cc_final: 0.6404 (m-80) REVERT: A 68 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7028 (mm-30) REVERT: A 70 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7113 (ptp90) REVERT: A 185 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.7212 (ttm-80) REVERT: A 304 GLU cc_start: 0.7350 (pm20) cc_final: 0.7050 (mp0) REVERT: A 478 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7857 (mtm180) REVERT: A 529 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9098 (mp) REVERT: B 185 ARG cc_start: 0.7679 (ttp-170) cc_final: 0.7304 (ttm-80) REVERT: B 304 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6996 (pm20) REVERT: B 529 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9095 (mp) outliers start: 15 outliers final: 6 residues processed: 115 average time/residue: 1.4272 time to fit residues: 172.9455 Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 28 optimal weight: 0.1980 chunk 44 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7678 Z= 0.146 Angle : 0.494 6.606 10420 Z= 0.257 Chirality : 0.037 0.121 1228 Planarity : 0.004 0.037 1202 Dihedral : 12.664 141.041 1620 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.92 % Allowed : 15.98 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.44 (0.29), residues: 876 helix: 2.42 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.66 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 285 HIS 0.001 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.015 0.002 TYR A 195 ARG 0.010 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.883 Fit side-chains REVERT: A 68 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: A 70 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7145 (ptp90) REVERT: A 185 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.7213 (ttm-80) REVERT: A 304 GLU cc_start: 0.7360 (pm20) cc_final: 0.7061 (mp0) REVERT: A 478 ARG cc_start: 0.8164 (mtp180) cc_final: 0.7867 (mtm180) REVERT: A 529 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9107 (mp) REVERT: B 185 ARG cc_start: 0.7680 (ttp-170) cc_final: 0.7309 (ttm-80) REVERT: B 304 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: B 529 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9104 (mp) outliers start: 13 outliers final: 8 residues processed: 108 average time/residue: 1.3846 time to fit residues: 157.4978 Evaluate side-chains 113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 0.0870 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7678 Z= 0.143 Angle : 0.493 6.656 10420 Z= 0.256 Chirality : 0.037 0.123 1228 Planarity : 0.004 0.038 1202 Dihedral : 12.480 133.969 1620 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.92 % Allowed : 16.24 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.49 (0.29), residues: 876 helix: 2.46 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.66 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 285 HIS 0.001 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.014 0.002 TYR A 195 ARG 0.010 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.829 Fit side-chains REVERT: A 32 ARG cc_start: 0.7282 (mpt-90) cc_final: 0.7039 (mtp85) REVERT: A 68 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6969 (mm-30) REVERT: A 185 ARG cc_start: 0.7682 (ttp-170) cc_final: 0.7218 (ttm-80) REVERT: A 304 GLU cc_start: 0.7376 (pm20) cc_final: 0.7065 (mp0) REVERT: B 70 ARG cc_start: 0.6938 (mpp80) cc_final: 0.6636 (mpp-170) REVERT: B 185 ARG cc_start: 0.7683 (ttp-170) cc_final: 0.7300 (ttm-80) REVERT: B 529 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9089 (mp) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 1.3879 time to fit residues: 161.2003 Evaluate side-chains 109 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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: 0.8670 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7678 Z= 0.242 Angle : 0.574 7.780 10420 Z= 0.294 Chirality : 0.041 0.137 1228 Planarity : 0.004 0.042 1202 Dihedral : 12.871 116.953 1620 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.66 % Allowed : 15.98 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.28), residues: 876 helix: 2.15 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.73 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 499 HIS 0.003 0.001 HIS A 200 PHE 0.014 0.002 PHE B 196 TYR 0.017 0.002 TYR A 195 ARG 0.010 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.802 Fit side-chains REVERT: A 61 PHE cc_start: 0.7120 (m-10) cc_final: 0.6609 (m-80) REVERT: A 68 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7010 (mm-30) REVERT: A 185 ARG cc_start: 0.7706 (ttp-170) cc_final: 0.7257 (ttm-80) REVERT: A 304 GLU cc_start: 0.7406 (pm20) cc_final: 0.7072 (mp0) REVERT: B 185 ARG cc_start: 0.7711 (ttp-170) cc_final: 0.7324 (ttm-80) REVERT: B 295 GLU cc_start: 0.7675 (mp0) cc_final: 0.7425 (mp0) REVERT: B 304 GLU cc_start: 0.7378 (pm20) cc_final: 0.7001 (mp0) REVERT: B 529 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9112 (mp) outliers start: 11 outliers final: 6 residues processed: 111 average time/residue: 1.3396 time to fit residues: 157.1524 Evaluate side-chains 111 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.8642 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7678 Z= 0.165 Angle : 0.517 7.625 10420 Z= 0.267 Chirality : 0.038 0.129 1228 Planarity : 0.004 0.038 1202 Dihedral : 12.631 118.991 1620 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.41 % Allowed : 16.88 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.29), residues: 876 helix: 2.33 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.70 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 499 HIS 0.002 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.015 0.002 TYR A 195 ARG 0.011 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.689 Fit side-chains REVERT: A 32 ARG cc_start: 0.7292 (mpt-90) cc_final: 0.7053 (mtp85) REVERT: A 61 PHE cc_start: 0.7042 (m-10) cc_final: 0.6491 (m-80) REVERT: A 68 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7011 (mm-30) REVERT: A 70 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7235 (ptp90) REVERT: A 185 ARG cc_start: 0.7689 (ttp-170) cc_final: 0.7227 (ttm-80) REVERT: A 304 GLU cc_start: 0.7396 (pm20) cc_final: 0.7080 (mp0) REVERT: B 185 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7304 (ttm-80) outliers start: 9 outliers final: 6 residues processed: 108 average time/residue: 1.3690 time to fit residues: 155.8396 Evaluate side-chains 110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 0.0020 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 0.0970 overall best weight: 0.3386 ------------------------------------------------------------------------------- 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: 0.8594 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7678 Z= 0.123 Angle : 0.474 7.031 10420 Z= 0.245 Chirality : 0.037 0.121 1228 Planarity : 0.004 0.037 1202 Dihedral : 12.329 123.138 1620 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.28 % Allowed : 17.01 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.63 (0.29), residues: 876 helix: 2.57 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.65 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 285 HIS 0.001 0.000 HIS A 200 PHE 0.012 0.001 PHE B 196 TYR 0.013 0.001 TYR B 195 ARG 0.010 0.001 ARG B 528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.683 Fit side-chains REVERT: A 32 ARG cc_start: 0.7254 (mpt-90) cc_final: 0.7014 (mtp85) REVERT: A 185 ARG cc_start: 0.7665 (ttp-170) cc_final: 0.7204 (ttm-80) REVERT: A 304 GLU cc_start: 0.7388 (pm20) cc_final: 0.7081 (mp0) REVERT: B 185 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7291 (ttm-80) outliers start: 8 outliers final: 6 residues processed: 105 average time/residue: 1.3517 time to fit residues: 149.6120 Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 chunk 71 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.122980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.094351 restraints weight = 9664.103| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.43 r_work: 0.2826 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7678 Z= 0.141 Angle : 0.490 7.688 10420 Z= 0.253 Chirality : 0.037 0.123 1228 Planarity : 0.004 0.037 1202 Dihedral : 12.287 122.697 1620 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.02 % Allowed : 16.88 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.62 (0.29), residues: 876 helix: 2.56 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.61 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 499 HIS 0.001 0.000 HIS A 200 PHE 0.013 0.001 PHE B 196 TYR 0.014 0.002 TYR A 195 ARG 0.010 0.001 ARG B 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3593.36 seconds wall clock time: 65 minutes 6.53 seconds (3906.53 seconds total)