Starting phenix.real_space_refine on Mon Mar 11 12:38:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3o_24142/03_2024/7n3o_24142.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3o_24142/03_2024/7n3o_24142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3o_24142/03_2024/7n3o_24142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3o_24142/03_2024/7n3o_24142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3o_24142/03_2024/7n3o_24142.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3o_24142/03_2024/7n3o_24142.pdb" } resolution = 3.8 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= 0.002 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 222 5.49 5 S 12 5.16 5 C 4378 2.51 5 N 1500 2.21 5 O 2183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 518": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8295 Number of models: 1 Model: "" Number of chains: 2 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: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 4734 Classifications: {'RNA': 222} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 15, 'rna3p_pur': 99, 'rna3p_pyr': 91} Link IDs: {'rna2p': 32, 'rna3p': 189} Chain breaks: 4 Time building chain proxies: 5.27, per 1000 atoms: 0.64 Number of scatterers: 8295 At special positions: 0 Unit cell: (97.65, 105, 118.65, 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 222 15.00 O 2183 8.00 N 1500 7.00 C 4378 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: 4.49 Conformation dependent library (CDL) restraints added in 825.1 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 2 sheets defined 59.5% alpha, 11.0% beta 71 base pairs and 121 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 Processing helix chain 'A' and resid 27 through 42 Processing helix chain 'A' and resid 44 through 51 removed outlier: 4.113A pdb=" N GLN A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 4.076A pdb=" N VAL A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.506A pdb=" N THR A 68 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 102 Processing helix chain 'A' and resid 318 through 338 removed outlier: 4.455A pdb=" N HIS A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TRP A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 383 through 406 Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.632A pdb=" N ASN A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.535A pdb=" N LEU A 481 " --> pdb=" O ILE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 505 removed outlier: 3.860A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 538 removed outlier: 3.846A pdb=" N HIS A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 567 Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 589 through 605 Processing helix chain 'A' and resid 618 through 637 Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 284 removed outlier: 3.648A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU A 301 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 475 removed outlier: 3.625A pdb=" N GLY A 611 " --> pdb=" O LEU A 545 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 181 hydrogen bonds 342 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 121 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1019 1.33 - 1.45: 3605 1.45 - 1.57: 3841 1.57 - 1.69: 439 1.69 - 1.81: 18 Bond restraints: 8922 Sorted by residual: bond pdb=" N LEU A 308 " pdb=" CA LEU A 308 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.06e+00 bond pdb=" N THR A 387 " pdb=" CA THR A 387 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.28e-02 6.10e+03 6.94e+00 bond pdb=" O3' G B 56 " pdb=" P G B 57 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.68e+00 bond pdb=" C PRO A 280 " pdb=" O PRO A 280 " ideal model delta sigma weight residual 1.234 1.204 0.029 1.14e-02 7.69e+03 6.67e+00 bond pdb=" N VAL A 284 " pdb=" CA VAL A 284 " ideal model delta sigma weight residual 1.449 1.494 -0.046 1.80e-02 3.09e+03 6.43e+00 ... (remaining 8917 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.11: 1253 106.11 - 113.10: 5103 113.10 - 120.09: 3234 120.09 - 127.08: 3043 127.08 - 134.08: 519 Bond angle restraints: 13152 Sorted by residual: angle pdb=" CA VAL A 284 " pdb=" C VAL A 284 " pdb=" O VAL A 284 " ideal model delta sigma weight residual 121.68 117.41 4.27 7.90e-01 1.60e+00 2.92e+01 angle pdb=" O3' G B 56 " pdb=" C3' G B 56 " pdb=" C2' G B 56 " ideal model delta sigma weight residual 109.50 116.75 -7.25 1.50e+00 4.44e-01 2.34e+01 angle pdb=" CA PHE A 285 " pdb=" C PHE A 285 " pdb=" N GLU A 286 " ideal model delta sigma weight residual 115.81 121.14 -5.33 1.15e+00 7.56e-01 2.15e+01 angle pdb=" CA PHE A 285 " pdb=" CB PHE A 285 " pdb=" CG PHE A 285 " ideal model delta sigma weight residual 113.80 117.63 -3.83 1.00e+00 1.00e+00 1.47e+01 angle pdb=" CA PHE A 285 " pdb=" C PHE A 285 " pdb=" O PHE A 285 " ideal model delta sigma weight residual 120.63 116.66 3.97 1.05e+00 9.07e-01 1.43e+01 ... (remaining 13147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 4996 35.84 - 71.67: 558 71.67 - 107.51: 66 107.51 - 143.34: 4 143.34 - 179.18: 8 Dihedral angle restraints: 5632 sinusoidal: 4309 harmonic: 1323 Sorted by residual: 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 24.17 175.83 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U B 60 " pdb=" C1' U B 60 " pdb=" N1 U B 60 " pdb=" C2 U B 60 " ideal model delta sinusoidal sigma weight residual 232.00 52.82 179.18 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 98 " pdb=" C1' U B 98 " pdb=" N1 U B 98 " pdb=" C2 U B 98 " ideal model delta sinusoidal sigma weight residual 232.00 64.46 167.54 1 1.70e+01 3.46e-03 6.57e+01 ... (remaining 5629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1557 0.068 - 0.135: 81 0.135 - 0.203: 18 0.203 - 0.270: 5 0.270 - 0.338: 3 Chirality restraints: 1664 Sorted by residual: 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 -2.41 -0.34 2.00e-01 2.50e+01 2.85e+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 -2.73 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" P G B 56 " pdb=" OP1 G B 56 " pdb=" OP2 G B 56 " pdb=" O5' G B 56 " both_signs ideal model delta sigma weight residual True 2.41 -2.73 -0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1661 not shown) Planarity restraints: 850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 281 " 0.014 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C PHE A 281 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE A 281 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO A 282 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 45 " 0.031 2.00e-02 2.50e+03 1.52e-02 5.17e+00 pdb=" N1 U B 45 " -0.027 2.00e-02 2.50e+03 pdb=" C2 U B 45 " -0.009 2.00e-02 2.50e+03 pdb=" O2 U B 45 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U B 45 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U B 45 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U B 45 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U B 45 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U B 45 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 613 " -0.033 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 614 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 614 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 614 " -0.027 5.00e-02 4.00e+02 ... (remaining 847 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2008 2.81 - 3.33: 7404 3.33 - 3.85: 16020 3.85 - 4.38: 18102 4.38 - 4.90: 25371 Nonbonded interactions: 68905 Sorted by model distance: nonbonded pdb=" O2' U B 89 " pdb=" OP1 U B 90 " model vdw 2.285 2.440 nonbonded pdb=" O ALA A 25 " pdb=" OG1 THR A 29 " model vdw 2.286 2.440 nonbonded pdb=" O2 C B 28 " pdb=" N2 G B 31 " model vdw 2.301 2.520 nonbonded pdb=" O PHE A 72 " pdb=" OH TYR A 80 " model vdw 2.311 2.440 nonbonded pdb=" NE2 GLN A 560 " pdb=" OE2 GLU A 564 " model vdw 2.315 2.520 ... (remaining 68900 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.480 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: 2.180 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 30.530 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 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 0.046 8922 Z= 0.182 Angle : 0.594 7.679 13152 Z= 0.336 Chirality : 0.038 0.338 1664 Planarity : 0.004 0.049 850 Dihedral : 23.642 179.181 4774 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.35 % Allowed : 0.54 % Favored : 98.11 % 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: 1.09 (0.39), residues: 446 helix: 2.17 (0.33), residues: 239 sheet: -0.31 (0.61), residues: 75 loop : -1.39 (0.46), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 324 HIS 0.003 0.001 HIS A 42 PHE 0.009 0.001 PHE A 313 TYR 0.016 0.002 TYR A 441 ARG 0.008 0.001 ARG A 17 *********************** 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 81 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.546 Fit side-chains REVERT: A 603 GLN cc_start: 0.8122 (mt0) cc_final: 0.7730 (tt0) REVERT: A 625 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8032 (tm-30) REVERT: A 626 LEU cc_start: 0.8058 (tp) cc_final: 0.7827 (tp) outliers start: 5 outliers final: 0 residues processed: 79 average time/residue: 0.1725 time to fit residues: 19.7686 Evaluate side-chains 58 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 0.0370 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8922 Z= 0.154 Angle : 0.553 10.144 13152 Z= 0.276 Chirality : 0.031 0.190 1664 Planarity : 0.004 0.031 850 Dihedral : 24.007 179.245 3938 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.81 % Allowed : 12.16 % Favored : 87.03 % 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: 1.49 (0.40), residues: 446 helix: 2.41 (0.33), residues: 249 sheet: -0.29 (0.60), residues: 76 loop : -1.24 (0.50), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 324 HIS 0.003 0.001 HIS A 323 PHE 0.011 0.001 PHE A 281 TYR 0.022 0.002 TYR A 474 ARG 0.005 0.000 ARG A 17 *********************** 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 69 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.595 Fit side-chains REVERT: A 320 ARG cc_start: 0.7409 (ptp-110) cc_final: 0.6866 (ptp-170) REVERT: A 349 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7458 (mt) outliers start: 3 outliers final: 0 residues processed: 67 average time/residue: 0.1803 time to fit residues: 17.3296 Evaluate side-chains 61 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8922 Z= 0.300 Angle : 0.713 11.084 13152 Z= 0.361 Chirality : 0.039 0.215 1664 Planarity : 0.005 0.039 850 Dihedral : 24.230 175.339 3938 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.97 % Allowed : 18.38 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.39), residues: 446 helix: 1.55 (0.32), residues: 248 sheet: 0.18 (0.65), residues: 61 loop : -1.61 (0.47), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 324 HIS 0.006 0.001 HIS A 370 PHE 0.011 0.002 PHE A 313 TYR 0.018 0.002 TYR A 316 ARG 0.004 0.001 ARG A 492 *********************** 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 78 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7777 (mm-30) outliers start: 11 outliers final: 5 residues processed: 71 average time/residue: 0.2538 time to fit residues: 25.5609 Evaluate side-chains 62 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 559 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 342 HIS A 370 HIS A 379 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8922 Z= 0.325 Angle : 0.721 10.045 13152 Z= 0.363 Chirality : 0.039 0.247 1664 Planarity : 0.005 0.050 850 Dihedral : 24.306 179.225 3938 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.86 % Allowed : 21.35 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.39), residues: 446 helix: 1.55 (0.32), residues: 248 sheet: -0.35 (0.61), residues: 65 loop : -1.35 (0.50), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 21 HIS 0.007 0.001 HIS A 323 PHE 0.012 0.002 PHE A 313 TYR 0.023 0.002 TYR A 570 ARG 0.006 0.001 ARG A 391 *********************** 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 75 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8386 (tt) REVERT: A 435 ARG cc_start: 0.8077 (mtt-85) cc_final: 0.7374 (mtt-85) REVERT: A 550 ASP cc_start: 0.7200 (p0) cc_final: 0.6950 (p0) REVERT: A 551 MET cc_start: 0.6489 (OUTLIER) cc_final: 0.6173 (ppp) REVERT: A 565 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7634 (tm-30) outliers start: 18 outliers final: 8 residues processed: 68 average time/residue: 0.1814 time to fit residues: 17.8632 Evaluate side-chains 63 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8922 Z= 0.221 Angle : 0.626 10.705 13152 Z= 0.315 Chirality : 0.035 0.215 1664 Planarity : 0.004 0.049 850 Dihedral : 24.232 179.218 3938 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.68 % Allowed : 22.43 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.39), residues: 446 helix: 1.72 (0.32), residues: 250 sheet: -0.44 (0.59), residues: 67 loop : -1.34 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.003 0.001 HIS A 323 PHE 0.014 0.002 PHE A 328 TYR 0.023 0.002 TYR A 91 ARG 0.007 0.000 ARG A 391 *********************** 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 80 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 59 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7492 (mtt-85) REVERT: A 551 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.6103 (ppp) REVERT: A 565 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7586 (tm-30) outliers start: 21 outliers final: 9 residues processed: 73 average time/residue: 0.1607 time to fit residues: 17.3038 Evaluate side-chains 65 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 366 TRP Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 585 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.0060 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8922 Z= 0.191 Angle : 0.608 11.351 13152 Z= 0.304 Chirality : 0.034 0.190 1664 Planarity : 0.004 0.040 850 Dihedral : 24.156 179.024 3938 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.86 % Allowed : 24.32 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.39), residues: 446 helix: 1.91 (0.33), residues: 250 sheet: -0.48 (0.58), residues: 67 loop : -1.21 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 21 HIS 0.003 0.001 HIS A 323 PHE 0.012 0.001 PHE A 328 TYR 0.029 0.002 TYR A 570 ARG 0.009 0.000 ARG A 391 *********************** 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 78 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8099 (t-100) cc_final: 0.7670 (t60) REVERT: A 280 PRO cc_start: 0.8374 (Cg_exo) cc_final: 0.8001 (Cg_endo) REVERT: A 388 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 405 MET cc_start: 0.2730 (mmm) cc_final: 0.1949 (mmp) REVERT: A 435 ARG cc_start: 0.7837 (mtt-85) cc_final: 0.7436 (mtt-85) REVERT: A 551 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5968 (ppp) REVERT: A 565 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7575 (tm-30) outliers start: 18 outliers final: 11 residues processed: 72 average time/residue: 0.1667 time to fit residues: 17.6748 Evaluate side-chains 72 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8922 Z= 0.207 Angle : 0.609 10.632 13152 Z= 0.306 Chirality : 0.034 0.193 1664 Planarity : 0.004 0.042 850 Dihedral : 24.186 179.217 3938 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.22 % Allowed : 22.97 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.39), residues: 446 helix: 1.81 (0.32), residues: 250 sheet: -0.74 (0.58), residues: 65 loop : -1.09 (0.51), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 324 HIS 0.008 0.001 HIS A 323 PHE 0.013 0.002 PHE A 328 TYR 0.029 0.002 TYR A 91 ARG 0.005 0.000 ARG A 391 *********************** 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 83 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 60 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8133 (t-100) cc_final: 0.7744 (t60) REVERT: A 388 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7961 (mm-30) REVERT: A 435 ARG cc_start: 0.7838 (mtt-85) cc_final: 0.7411 (mtt-85) REVERT: A 551 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.5963 (ppp) REVERT: A 565 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7525 (tm-30) outliers start: 23 outliers final: 14 residues processed: 78 average time/residue: 0.1769 time to fit residues: 20.0229 Evaluate side-chains 69 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 598 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 0.0670 chunk 47 optimal weight: 10.0000 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.6978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8922 Z= 0.379 Angle : 0.778 11.307 13152 Z= 0.391 Chirality : 0.042 0.211 1664 Planarity : 0.005 0.046 850 Dihedral : 24.558 178.404 3938 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.41 % Allowed : 24.86 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.38), residues: 446 helix: 1.17 (0.32), residues: 250 sheet: -0.87 (0.58), residues: 65 loop : -1.21 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 324 HIS 0.005 0.001 HIS A 586 PHE 0.015 0.002 PHE A 313 TYR 0.018 0.002 TYR A 538 ARG 0.004 0.001 ARG A 391 *********************** 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 75 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8189 (mm-30) REVERT: A 435 ARG cc_start: 0.8024 (mtt-85) cc_final: 0.7779 (mtt-85) outliers start: 20 outliers final: 14 residues processed: 68 average time/residue: 0.1670 time to fit residues: 16.7210 Evaluate side-chains 66 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 585 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 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 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8922 Z= 0.186 Angle : 0.630 12.154 13152 Z= 0.315 Chirality : 0.035 0.190 1664 Planarity : 0.004 0.043 850 Dihedral : 24.320 178.071 3938 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.24 % Allowed : 28.38 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.40), residues: 446 helix: 1.72 (0.33), residues: 250 sheet: -0.67 (0.57), residues: 67 loop : -0.90 (0.52), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 382 HIS 0.004 0.001 HIS A 323 PHE 0.016 0.002 PHE A 328 TYR 0.013 0.001 TYR A 474 ARG 0.007 0.001 ARG A 592 *********************** 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 70 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7949 (t-100) cc_final: 0.7600 (t60) REVERT: A 388 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8074 (mm-30) REVERT: A 551 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.6144 (ppp) outliers start: 12 outliers final: 9 residues processed: 66 average time/residue: 0.1732 time to fit residues: 16.7686 Evaluate side-chains 65 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 585 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8922 Z= 0.196 Angle : 0.631 11.699 13152 Z= 0.316 Chirality : 0.035 0.192 1664 Planarity : 0.004 0.041 850 Dihedral : 24.241 177.510 3938 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.43 % Allowed : 28.65 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.40), residues: 446 helix: 1.76 (0.33), residues: 250 sheet: -0.73 (0.58), residues: 65 loop : -0.78 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 324 HIS 0.005 0.001 HIS A 323 PHE 0.015 0.001 PHE A 281 TYR 0.012 0.001 TYR A 538 ARG 0.008 0.000 ARG A 592 ********************** 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 66 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7943 (t-100) cc_final: 0.7577 (t60) REVERT: A 388 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8051 (mm-30) outliers start: 9 outliers final: 8 residues processed: 64 average time/residue: 0.1828 time to fit residues: 16.6939 Evaluate side-chains 64 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 583 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.157825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.123115 restraints weight = 18190.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123116 restraints weight = 11448.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.124453 restraints weight = 9273.880| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8922 Z= 0.211 Angle : 0.632 11.799 13152 Z= 0.317 Chirality : 0.035 0.195 1664 Planarity : 0.004 0.043 850 Dihedral : 24.226 176.414 3938 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.70 % Allowed : 28.65 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.40), residues: 446 helix: 1.77 (0.33), residues: 249 sheet: -0.80 (0.58), residues: 65 loop : -0.74 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 324 HIS 0.005 0.001 HIS A 323 PHE 0.011 0.002 PHE A 328 TYR 0.009 0.001 TYR A 474 ARG 0.004 0.000 ARG A 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1365.46 seconds wall clock time: 25 minutes 55.88 seconds (1555.88 seconds total)