Starting phenix.real_space_refine (version: dev) on Mon Apr 4 21:02:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3p_24143/04_2022/7n3p_24143.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3p_24143/04_2022/7n3p_24143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3p_24143/04_2022/7n3p_24143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3p_24143/04_2022/7n3p_24143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3p_24143/04_2022/7n3p_24143.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3p_24143/04_2022/7n3p_24143.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.108 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 358": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 9055 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3561 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 16, 'TRANS': 437} Chain breaks: 3 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 14, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 4883 Classifications: {'RNA': 229} Modifications used: {'rna3p_pyr': 95, 'rna2p_pur': 17, 'rna3p_pur': 103, 'rna2p_pyr': 14} Link IDs: {'rna3p': 197, 'rna2p': 31} Chain breaks: 4 Chain: "C" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 399 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Time building chain proxies: 5.99, per 1000 atoms: 0.66 Number of scatterers: 9055 At special positions: 0 Unit cell: (100.8, 105, 124.95, 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 259 15.00 O 2413 8.00 N 1634 7.00 C 4737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 580.4 milliseconds 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 858 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 58.6% alpha, 11.9% beta 80 base pairs and 151 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.651A pdb=" N ARG A 17 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 41 Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 57 through 68 Proline residue: A 65 - end of helix removed outlier: 3.896A pdb=" N THR A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 102 Processing helix chain 'A' and resid 321 through 338 removed outlier: 3.752A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.785A pdb=" N LEU A 346 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 406 removed outlier: 3.700A pdb=" N GLU A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 429 removed outlier: 3.656A pdb=" N THR A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 485 through 505 removed outlier: 3.696A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 538 Processing helix chain 'A' and resid 550 through 567 Processing helix chain 'A' and resid 570 through 585 removed outlier: 3.519A pdb=" N GLN A 574 " --> pdb=" O TYR A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 605 removed outlier: 3.969A pdb=" N LEU A 593 " --> pdb=" O SER A 589 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 637 Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285 removed outlier: 6.389A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 295 Processing sheet with id=AA3, first strand: chain 'A' and resid 471 through 475 removed outlier: 3.665A pdb=" N ALA A 473 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER A 445 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER A 542 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 447 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL A 544 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 449 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 607 " --> pdb=" O GLY A 541 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 203 hydrogen bonds 380 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 151 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 4.87 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: 1456 1.33 - 1.45: 3855 1.45 - 1.57: 3931 1.57 - 1.69: 511 1.69 - 1.81: 18 Bond restraints: 9771 Sorted by residual: bond pdb=" O5' G B 57 " pdb=" C5' G B 57 " ideal model delta sigma weight residual 1.420 1.454 -0.034 1.50e-02 4.44e+03 5.25e+00 bond pdb=" P G B 224 " pdb=" OP2 G B 224 " ideal model delta sigma weight residual 1.485 1.524 -0.039 2.00e-02 2.50e+03 3.87e+00 bond pdb=" O5' G B 224 " pdb=" C5' G B 224 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.83e+00 bond pdb=" O5' G B 56 " pdb=" C5' G B 56 " ideal model delta sigma weight residual 1.424 1.453 -0.029 1.50e-02 4.44e+03 3.77e+00 bond pdb=" P G B 56 " pdb=" OP2 G B 56 " ideal model delta sigma weight residual 1.485 1.523 -0.038 2.00e-02 2.50e+03 3.69e+00 ... (remaining 9766 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.62: 1581 106.62 - 113.47: 5617 113.47 - 120.31: 3630 120.31 - 127.15: 3058 127.15 - 133.99: 573 Bond angle restraints: 14459 Sorted by residual: angle pdb=" O3' G B 56 " pdb=" C3' G B 56 " pdb=" C2' G B 56 " ideal model delta sigma weight residual 109.50 116.76 -7.26 1.50e+00 4.44e-01 2.34e+01 angle pdb=" O3' G B 189 " pdb=" C3' G B 189 " pdb=" C2' G B 189 " ideal model delta sigma weight residual 109.50 116.52 -7.02 1.50e+00 4.44e-01 2.19e+01 angle pdb=" C4' G B 56 " pdb=" C3' G B 56 " pdb=" O3' G B 56 " ideal model delta sigma weight residual 109.40 115.70 -6.30 1.50e+00 4.44e-01 1.76e+01 angle pdb=" C4' G B 189 " pdb=" C3' G B 189 " pdb=" O3' G B 189 " ideal model delta sigma weight residual 109.40 114.53 -5.13 1.50e+00 4.44e-01 1.17e+01 angle pdb=" N GLY A 569 " pdb=" CA GLY A 569 " pdb=" C GLY A 569 " ideal model delta sigma weight residual 113.18 120.19 -7.01 2.37e+00 1.78e-01 8.75e+00 ... (remaining 14454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 4881 35.08 - 70.15: 302 70.15 - 105.23: 18 105.23 - 140.30: 2 140.30 - 175.38: 11 Dihedral angle restraints: 5214 sinusoidal: 3891 harmonic: 1323 Sorted by residual: dihedral pdb=" C4' G B 189 " pdb=" C3' G B 189 " pdb=" C2' G B 189 " pdb=" C1' G B 189 " ideal model delta sinusoidal sigma weight residual -35.00 32.64 -67.64 1 8.00e+00 1.56e-02 9.29e+01 dihedral pdb=" C5' G B 189 " pdb=" C4' G B 189 " pdb=" C3' G B 189 " pdb=" O3' G B 189 " ideal model delta sinusoidal sigma weight residual 147.00 79.79 67.21 1 8.00e+00 1.56e-02 9.19e+01 dihedral pdb=" O4' C B 196 " pdb=" C1' C B 196 " pdb=" N1 C B 196 " pdb=" C2 C B 196 " ideal model delta sinusoidal sigma weight residual 200.00 26.02 173.98 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 5211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1753 0.083 - 0.165: 54 0.165 - 0.248: 7 0.248 - 0.330: 3 0.330 - 0.413: 2 Chirality restraints: 1819 Sorted by residual: chirality pdb=" C3' G B 189 " pdb=" C4' G B 189 " pdb=" O3' G B 189 " pdb=" C2' G B 189 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C3' G B 56 " pdb=" C4' G B 56 " pdb=" O3' G B 56 " pdb=" C2' G B 56 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" P G B 57 " pdb=" OP1 G B 57 " pdb=" OP2 G B 57 " pdb=" O5' G B 57 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1816 not shown) Planarity restraints: 887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 96 " 0.025 2.00e-02 2.50e+03 1.54e-02 5.33e+00 pdb=" N1 C B 96 " -0.032 2.00e-02 2.50e+03 pdb=" C2 C B 96 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C B 96 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C B 96 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C B 96 " 0.020 2.00e-02 2.50e+03 pdb=" N4 C B 96 " -0.004 2.00e-02 2.50e+03 pdb=" C5 C B 96 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C B 96 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 97 " 0.030 2.00e-02 2.50e+03 1.51e-02 5.16e+00 pdb=" N1 C B 97 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C B 97 " -0.006 2.00e-02 2.50e+03 pdb=" O2 C B 97 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C B 97 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C B 97 " 0.007 2.00e-02 2.50e+03 pdb=" N4 C B 97 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C B 97 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C B 97 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 45 " 0.029 2.00e-02 2.50e+03 1.46e-02 4.81e+00 pdb=" N1 U B 45 " -0.030 2.00e-02 2.50e+03 pdb=" C2 U B 45 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U B 45 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U B 45 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U B 45 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 45 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U B 45 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U B 45 " -0.009 2.00e-02 2.50e+03 ... (remaining 884 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1338 2.76 - 3.29: 8146 3.29 - 3.83: 18195 3.83 - 4.36: 20224 4.36 - 4.90: 28501 Nonbonded interactions: 76404 Sorted by model distance: nonbonded pdb=" O6 G B 165 " pdb=" O4 U B 173 " model vdw 2.224 2.432 nonbonded pdb=" O2' G B 189 " pdb=" O5' A B 190 " model vdw 2.266 2.440 nonbonded pdb=" O2' A B 190 " pdb=" O4' A B 191 " model vdw 2.284 2.440 nonbonded pdb=" O2 U B 30 " pdb=" N1 G B 31 " model vdw 2.288 2.520 nonbonded pdb=" ND2 ASN A 379 " pdb=" OE1 GLN A 603 " model vdw 2.294 2.520 ... (remaining 76399 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 259 5.49 5 S 12 5.16 5 C 4737 2.51 5 N 1634 2.21 5 O 2413 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 0.300 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: 2.570 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.080 Process input model: 32.360 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.003 0.039 9771 Z= 0.153 Angle : 0.580 8.191 14459 Z= 0.308 Chirality : 0.037 0.413 1819 Planarity : 0.003 0.047 887 Dihedral : 18.979 175.377 4356 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.40), residues: 446 helix: 2.21 (0.33), residues: 244 sheet: -0.00 (0.61), residues: 67 loop : -0.27 (0.55), residues: 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.642 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1886 time to fit residues: 17.1105 Evaluate side-chains 47 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.659 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 30.0000 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.042 9771 Z= 0.435 Angle : 0.705 7.814 14459 Z= 0.370 Chirality : 0.040 0.313 1819 Planarity : 0.005 0.060 887 Dihedral : 19.543 179.672 3520 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.40), residues: 446 helix: 2.04 (0.33), residues: 242 sheet: -0.15 (0.63), residues: 69 loop : -0.82 (0.51), residues: 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.630 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 48 average time/residue: 0.1609 time to fit residues: 12.1007 Evaluate side-chains 40 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0825 time to fit residues: 1.4523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9771 Z= 0.206 Angle : 0.550 7.726 14459 Z= 0.291 Chirality : 0.033 0.221 1819 Planarity : 0.004 0.047 887 Dihedral : 19.351 179.750 3520 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.41), residues: 446 helix: 2.37 (0.34), residues: 242 sheet: -0.08 (0.65), residues: 63 loop : -0.64 (0.51), residues: 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.640 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 51 average time/residue: 0.1662 time to fit residues: 13.1145 Evaluate side-chains 45 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0780 time to fit residues: 0.7895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 60 optimal weight: 50.0000 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 9771 Z= 0.284 Angle : 0.594 7.573 14459 Z= 0.314 Chirality : 0.036 0.213 1819 Planarity : 0.004 0.050 887 Dihedral : 19.537 179.573 3520 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.40), residues: 446 helix: 2.20 (0.33), residues: 242 sheet: -0.19 (0.64), residues: 64 loop : -0.75 (0.50), residues: 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.635 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 54 average time/residue: 0.1595 time to fit residues: 13.3698 Evaluate side-chains 47 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0836 time to fit residues: 1.6066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 60 optimal weight: 50.0000 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9771 Z= 0.271 Angle : 0.581 7.268 14459 Z= 0.306 Chirality : 0.035 0.230 1819 Planarity : 0.004 0.045 887 Dihedral : 19.531 179.959 3520 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.40), residues: 446 helix: 2.20 (0.33), residues: 242 sheet: -0.23 (0.66), residues: 63 loop : -0.83 (0.50), residues: 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.703 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 50 average time/residue: 0.1627 time to fit residues: 12.6703 Evaluate side-chains 47 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.610 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0901 time to fit residues: 1.4720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.127 9771 Z= 0.355 Angle : 0.643 7.986 14459 Z= 0.338 Chirality : 0.038 0.223 1819 Planarity : 0.005 0.094 887 Dihedral : 19.701 179.781 3520 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.40), residues: 446 helix: 1.96 (0.33), residues: 242 sheet: -0.32 (0.63), residues: 64 loop : -1.15 (0.48), residues: 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.571 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.1648 time to fit residues: 12.7215 Evaluate side-chains 48 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.577 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0840 time to fit residues: 1.3132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 42 optimal weight: 0.0370 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.105 9771 Z= 0.155 Angle : 0.532 8.493 14459 Z= 0.280 Chirality : 0.032 0.184 1819 Planarity : 0.005 0.095 887 Dihedral : 19.264 178.387 3520 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.41), residues: 446 helix: 2.46 (0.34), residues: 242 sheet: -0.21 (0.65), residues: 63 loop : -0.73 (0.50), residues: 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.597 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 52 average time/residue: 0.1483 time to fit residues: 12.4601 Evaluate side-chains 50 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.642 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 61 optimal weight: 40.0000 chunk 64 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN A 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.124 9771 Z= 0.426 Angle : 0.698 8.287 14459 Z= 0.365 Chirality : 0.040 0.234 1819 Planarity : 0.005 0.090 887 Dihedral : 19.709 178.903 3520 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.40), residues: 446 helix: 2.08 (0.33), residues: 242 sheet: -0.21 (0.64), residues: 64 loop : -1.22 (0.49), residues: 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.659 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 0.1422 time to fit residues: 10.5056 Evaluate side-chains 45 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0860 time to fit residues: 1.3297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 30.0000 chunk 62 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN A 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.138 9771 Z= 0.226 Angle : 0.576 10.666 14459 Z= 0.305 Chirality : 0.034 0.195 1819 Planarity : 0.005 0.094 887 Dihedral : 19.510 179.799 3520 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.41), residues: 446 helix: 2.30 (0.34), residues: 242 sheet: -0.26 (0.65), residues: 63 loop : -1.13 (0.49), residues: 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.637 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.1687 time to fit residues: 12.0419 Evaluate side-chains 43 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0824 time to fit residues: 0.9902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 30.0000 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 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 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.155 9771 Z= 0.194 Angle : 0.570 15.378 14459 Z= 0.303 Chirality : 0.033 0.191 1819 Planarity : 0.005 0.109 887 Dihedral : 19.369 178.645 3520 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.41), residues: 446 helix: 2.42 (0.34), residues: 242 sheet: -0.23 (0.64), residues: 63 loop : -0.99 (0.50), residues: 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.681 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1433 time to fit residues: 11.6497 Evaluate side-chains 45 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.133292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.093475 restraints weight = 20987.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096328 restraints weight = 8925.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097984 restraints weight = 5907.294| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.167 9771 Z= 0.247 Angle : 0.590 15.624 14459 Z= 0.313 Chirality : 0.034 0.198 1819 Planarity : 0.005 0.107 887 Dihedral : 19.392 179.997 3520 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.41), residues: 446 helix: 2.34 (0.34), residues: 242 sheet: -0.21 (0.64), residues: 63 loop : -1.05 (0.50), residues: 141 =============================================================================== Job complete usr+sys time: 1197.75 seconds wall clock time: 23 minutes 2.69 seconds (1382.69 seconds total)