Starting phenix.real_space_refine on Tue Feb 13 08:20:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnz_27585/02_2024/8dnz_27585_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnz_27585/02_2024/8dnz_27585.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnz_27585/02_2024/8dnz_27585_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnz_27585/02_2024/8dnz_27585_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnz_27585/02_2024/8dnz_27585_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnz_27585/02_2024/8dnz_27585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnz_27585/02_2024/8dnz_27585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnz_27585/02_2024/8dnz_27585_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnz_27585/02_2024/8dnz_27585_trim_updated.pdb" } resolution = 2.57 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= 0.003 sd= 0.055 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 2872 2.51 5 N 694 2.21 5 O 744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4337 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 251 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3548 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 58 Unusual residues: {'T69': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NMTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="T69 D 1 " pdbres="0A1 D 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'IML:plan-1': 1, 'MAA:plan-1': 2, '0A1:plan-2': 1, 'T69:plan-1': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.91, per 1000 atoms: 0.67 Number of scatterers: 4337 At special positions: 0 Unit cell: (93.45, 80.85, 78.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 744 8.00 N 694 7.00 C 2872 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 801.6 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1018 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 3 sheets defined 66.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 65 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 70 through 95 Processing helix chain 'A' and resid 5 through 8 No H-bonds generated for 'chain 'A' and resid 5 through 8' Processing helix chain 'A' and resid 10 through 13 No H-bonds generated for 'chain 'A' and resid 10 through 13' Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 106 through 134 Processing helix chain 'A' and resid 140 through 143 No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'A' and resid 145 through 171 Processing helix chain 'A' and resid 178 through 196 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 242 through 259 Processing helix chain 'A' and resid 289 through 311 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.752A pdb=" N TYR A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 344' Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 358 through 380 Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 410 through 437 Proline residue: A 418 - end of helix removed outlier: 3.543A pdb=" N SER A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 467 removed outlier: 3.540A pdb=" N ILE A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 200 through 202 Processing sheet with id= B, first strand: chain 'A' and resid 276 through 282 Processing sheet with id= C, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.190A pdb=" N SER A 325 " --> pdb=" O PRO A 337 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 2.13 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: 709 1.33 - 1.45: 1128 1.45 - 1.57: 2538 1.57 - 1.70: 9 1.70 - 1.82: 45 Bond restraints: 4429 Sorted by residual: bond pdb=" C34 T69 D 1 " pdb=" S01 T69 D 1 " ideal model delta sigma weight residual 1.444 1.818 -0.374 2.00e-02 2.50e+03 3.50e+02 bond pdb=" C26 T69 D 1 " pdb=" N12 T69 D 1 " ideal model delta sigma weight residual 1.629 1.350 0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C26 T69 D 1 " pdb=" S01 T69 D 1 " ideal model delta sigma weight residual 1.628 1.807 -0.179 2.00e-02 2.50e+03 8.05e+01 bond pdb=" CB 0A1 D 2 " pdb=" CG 0A1 D 2 " ideal model delta sigma weight residual 1.510 1.666 -0.156 2.00e-02 2.50e+03 6.10e+01 bond pdb=" C MAA D 3 " pdb=" N IML D 4 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.17e+01 ... (remaining 4424 not shown) Histogram of bond angle deviations from ideal: 95.20 - 102.95: 31 102.95 - 110.70: 1435 110.70 - 118.45: 2039 118.45 - 126.20: 2436 126.20 - 133.95: 56 Bond angle restraints: 5997 Sorted by residual: angle pdb=" CA MAA D 5 " pdb=" C MAA D 5 " pdb=" O MAA D 5 " ideal model delta sigma weight residual 120.80 107.21 13.59 1.70e+00 3.46e-01 6.39e+01 angle pdb=" C25 T69 D 1 " pdb=" C26 T69 D 1 " pdb=" N12 T69 D 1 " ideal model delta sigma weight residual 110.16 133.18 -23.02 3.00e+00 1.11e-01 5.89e+01 angle pdb=" N GLY A 442 " pdb=" CA GLY A 442 " pdb=" C GLY A 442 " ideal model delta sigma weight residual 113.58 106.52 7.06 1.07e+00 8.73e-01 4.35e+01 angle pdb=" CA 0A1 D 2 " pdb=" C 0A1 D 2 " pdb=" N MAA D 3 " ideal model delta sigma weight residual 116.20 127.09 -10.89 2.00e+00 2.50e-01 2.97e+01 angle pdb=" N 0A1 D 2 " pdb=" CA 0A1 D 2 " pdb=" CB 0A1 D 2 " ideal model delta sigma weight residual 110.50 119.64 -9.14 1.70e+00 3.46e-01 2.89e+01 ... (remaining 5992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.51: 2542 28.51 - 57.02: 65 57.02 - 85.53: 9 85.53 - 114.04: 0 114.04 - 142.55: 1 Dihedral angle restraints: 2617 sinusoidal: 1031 harmonic: 1586 Sorted by residual: dihedral pdb=" C15 T69 D 1 " pdb=" C17 T69 D 1 " pdb=" C18 T69 D 1 " pdb=" C19 T69 D 1 " ideal model delta sinusoidal sigma weight residual 147.71 5.16 142.55 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" CB MET A 77 " pdb=" CG MET A 77 " pdb=" SD MET A 77 " pdb=" CE MET A 77 " ideal model delta sinusoidal sigma weight residual 180.00 123.52 56.48 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA ASP A 389 " pdb=" CB ASP A 389 " pdb=" CG ASP A 389 " pdb=" OD1 ASP A 389 " ideal model delta sinusoidal sigma weight residual -30.00 -81.14 51.14 1 2.00e+01 2.50e-03 8.94e+00 ... (remaining 2614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.428: 709 0.428 - 0.856: 0 0.856 - 1.284: 0 1.284 - 1.712: 0 1.712 - 2.140: 1 Chirality restraints: 710 Sorted by residual: chirality pdb=" C26 T69 D 1 " pdb=" C25 T69 D 1 " pdb=" N12 T69 D 1 " pdb=" S01 T69 D 1 " both_signs ideal model delta sigma weight residual False 3.14 1.00 2.14 2.00e-01 2.50e+01 1.15e+02 chirality pdb=" CA IML D 4 " pdb=" N IML D 4 " pdb=" C IML D 4 " pdb=" CB IML D 4 " both_signs ideal model delta sigma weight residual False 2.43 2.84 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA MAA D 5 " pdb=" N MAA D 5 " pdb=" C MAA D 5 " pdb=" CB MAA D 5 " both_signs ideal model delta sigma weight residual False 2.48 2.78 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 707 not shown) Planarity restraints: 732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 439 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C GLY A 439 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY A 439 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 440 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 60 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A 61 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 21 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 22 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " -0.024 5.00e-02 4.00e+02 ... (remaining 729 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 123 2.72 - 3.27: 4633 3.27 - 3.81: 7338 3.81 - 4.36: 8946 4.36 - 4.90: 15331 Nonbonded interactions: 36371 Sorted by model distance: nonbonded pdb=" OD2 ASP A 139 " pdb=" OG SER A 141 " model vdw 2.177 2.440 nonbonded pdb=" O LEU A 181 " pdb=" OG1 THR A 185 " model vdw 2.285 2.440 nonbonded pdb=" O TYR A 131 " pdb=" OG1 THR A 134 " model vdw 2.310 2.440 nonbonded pdb=" N GLY A 74 " pdb=" OE1 GLU A 78 " model vdw 2.313 2.520 nonbonded pdb=" O ILE A 19 " pdb=" NZ LYS A 171 " model vdw 2.358 2.520 ... (remaining 36366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 3.660 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.090 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 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 : 0.010 0.374 4429 Z= 0.532 Angle : 0.756 23.015 5997 Z= 0.380 Chirality : 0.091 2.140 710 Planarity : 0.005 0.049 732 Dihedral : 13.569 142.547 1599 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.55 (0.35), residues: 543 helix: 1.69 (0.25), residues: 388 sheet: -1.32 (1.44), residues: 12 loop : -0.50 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.000 HIS C 88 PHE 0.017 0.001 PHE A 217 TYR 0.007 0.001 TYR A 137 ARG 0.006 0.001 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.464 Fit side-chains REVERT: B 31 LYS cc_start: 0.8113 (mppt) cc_final: 0.7711 (mppt) REVERT: A 27 GLN cc_start: 0.7407 (mm110) cc_final: 0.7001 (mm110) REVERT: A 117 LYS cc_start: 0.7491 (mttt) cc_final: 0.7201 (mtmm) REVERT: A 167 GLU cc_start: 0.7900 (tt0) cc_final: 0.7670 (tt0) REVERT: A 268 ARG cc_start: 0.6814 (ptp-110) cc_final: 0.6438 (ptm-80) REVERT: A 307 MET cc_start: 0.6089 (mmt) cc_final: 0.5278 (ttt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 1.5738 time to fit residues: 116.6886 Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.0270 chunk 16 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4429 Z= 0.190 Angle : 0.500 5.896 5997 Z= 0.253 Chirality : 0.038 0.131 710 Planarity : 0.004 0.037 732 Dihedral : 7.500 112.496 605 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.35), residues: 543 helix: 2.27 (0.25), residues: 390 sheet: -1.02 (1.56), residues: 12 loop : -0.48 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 90 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE B 49 TYR 0.009 0.001 TYR A 137 ARG 0.004 0.001 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.498 Fit side-chains REVERT: B 34 GLN cc_start: 0.7261 (mt0) cc_final: 0.6936 (mt0) REVERT: A 27 GLN cc_start: 0.7295 (mm110) cc_final: 0.6994 (mm110) REVERT: A 117 LYS cc_start: 0.7297 (mttt) cc_final: 0.7064 (mtmm) REVERT: A 268 ARG cc_start: 0.6934 (ptp-110) cc_final: 0.6376 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 1.3616 time to fit residues: 88.8242 Evaluate side-chains 59 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.0770 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.0170 chunk 48 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4429 Z= 0.183 Angle : 0.466 6.293 5997 Z= 0.235 Chirality : 0.038 0.146 710 Planarity : 0.004 0.035 732 Dihedral : 6.884 92.671 605 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.86 % Allowed : 9.91 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.35), residues: 543 helix: 2.42 (0.25), residues: 390 sheet: -0.84 (1.62), residues: 12 loop : -0.42 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.009 0.001 PHE B 33 TYR 0.008 0.001 TYR A 137 ARG 0.008 0.001 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.512 Fit side-chains REVERT: B 34 GLN cc_start: 0.7234 (mt0) cc_final: 0.6915 (mt0) REVERT: A 27 GLN cc_start: 0.7168 (mm110) cc_final: 0.6923 (mm110) REVERT: A 139 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7667 (t70) REVERT: A 268 ARG cc_start: 0.6990 (ptp-110) cc_final: 0.6673 (ptm160) REVERT: A 405 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6784 (mtt-85) outliers start: 4 outliers final: 1 residues processed: 62 average time/residue: 1.4035 time to fit residues: 90.0151 Evaluate side-chains 61 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 405 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4429 Z= 0.261 Angle : 0.506 7.369 5997 Z= 0.254 Chirality : 0.039 0.134 710 Planarity : 0.004 0.035 732 Dihedral : 7.073 92.311 605 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.51 % Allowed : 11.85 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.35), residues: 543 helix: 2.26 (0.25), residues: 392 sheet: -1.27 (1.39), residues: 14 loop : -0.35 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.011 0.002 PHE B 49 TYR 0.011 0.001 TYR A 137 ARG 0.007 0.001 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.426 Fit side-chains REVERT: B 34 GLN cc_start: 0.7345 (mt0) cc_final: 0.7029 (mt0) REVERT: A 27 GLN cc_start: 0.7194 (mm110) cc_final: 0.6924 (mm110) REVERT: A 139 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7719 (t70) REVERT: A 228 ARG cc_start: 0.7211 (ttp-170) cc_final: 0.6962 (ttp-170) REVERT: A 268 ARG cc_start: 0.7189 (ptp-110) cc_final: 0.6910 (ptm160) REVERT: A 405 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6820 (mtt-85) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 1.4755 time to fit residues: 88.4805 Evaluate side-chains 58 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.0010 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4429 Z= 0.185 Angle : 0.458 6.419 5997 Z= 0.230 Chirality : 0.038 0.131 710 Planarity : 0.004 0.035 732 Dihedral : 6.810 90.615 605 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.29 % Allowed : 13.58 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.36), residues: 543 helix: 2.44 (0.25), residues: 392 sheet: -0.93 (1.58), residues: 12 loop : -0.30 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.007 0.001 PHE B 33 TYR 0.007 0.001 TYR A 131 ARG 0.003 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.533 Fit side-chains REVERT: B 34 GLN cc_start: 0.7282 (mt0) cc_final: 0.6968 (mt0) REVERT: A 27 GLN cc_start: 0.7169 (mm110) cc_final: 0.6906 (mm110) REVERT: A 228 ARG cc_start: 0.7148 (ttp-170) cc_final: 0.6914 (ttp-170) REVERT: A 268 ARG cc_start: 0.7195 (ptp-110) cc_final: 0.6862 (ptm160) outliers start: 6 outliers final: 1 residues processed: 59 average time/residue: 1.5089 time to fit residues: 92.1865 Evaluate side-chains 57 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4429 Z= 0.220 Angle : 0.477 6.977 5997 Z= 0.238 Chirality : 0.038 0.130 710 Planarity : 0.004 0.035 732 Dihedral : 6.919 90.707 605 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.51 % Allowed : 13.36 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.35), residues: 543 helix: 2.40 (0.25), residues: 392 sheet: -1.01 (1.60), residues: 12 loop : -0.25 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.009 0.001 PHE B 49 TYR 0.008 0.001 TYR A 137 ARG 0.006 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.561 Fit side-chains REVERT: B 34 GLN cc_start: 0.7272 (mt0) cc_final: 0.6925 (mt0) REVERT: A 27 GLN cc_start: 0.7165 (mm110) cc_final: 0.6915 (mm110) REVERT: A 139 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7643 (t70) REVERT: A 228 ARG cc_start: 0.7157 (ttp-170) cc_final: 0.6909 (ttp-170) REVERT: A 268 ARG cc_start: 0.7204 (ptp-110) cc_final: 0.6805 (ptm160) outliers start: 7 outliers final: 3 residues processed: 58 average time/residue: 1.4423 time to fit residues: 86.5843 Evaluate side-chains 59 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4429 Z= 0.204 Angle : 0.467 6.723 5997 Z= 0.233 Chirality : 0.038 0.129 710 Planarity : 0.004 0.035 732 Dihedral : 6.866 89.896 605 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.86 % Allowed : 14.01 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.36), residues: 543 helix: 2.42 (0.25), residues: 393 sheet: -0.92 (1.64), residues: 12 loop : -0.18 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE B 49 TYR 0.011 0.001 TYR A 63 ARG 0.004 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.512 Fit side-chains REVERT: B 34 GLN cc_start: 0.7245 (mt0) cc_final: 0.6897 (mt0) REVERT: A 27 GLN cc_start: 0.7167 (mm110) cc_final: 0.6921 (mm110) REVERT: A 228 ARG cc_start: 0.7160 (ttp-170) cc_final: 0.6908 (ttp-170) REVERT: A 235 TYR cc_start: 0.7841 (m-80) cc_final: 0.7472 (m-80) REVERT: A 268 ARG cc_start: 0.7164 (ptp-110) cc_final: 0.6757 (ptm160) outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 1.4341 time to fit residues: 84.5594 Evaluate side-chains 59 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.0050 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4429 Z= 0.169 Angle : 0.446 6.313 5997 Z= 0.223 Chirality : 0.037 0.128 710 Planarity : 0.004 0.035 732 Dihedral : 6.693 87.980 605 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.65 % Allowed : 14.66 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.36), residues: 543 helix: 2.52 (0.26), residues: 393 sheet: -1.04 (1.61), residues: 12 loop : -0.13 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.007 0.001 PHE A 112 TYR 0.007 0.001 TYR A 131 ARG 0.004 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.484 Fit side-chains REVERT: B 34 GLN cc_start: 0.7181 (mt0) cc_final: 0.6868 (mt0) REVERT: C 86 MET cc_start: 0.7113 (mmp) cc_final: 0.6761 (mmm) REVERT: A 228 ARG cc_start: 0.7164 (ttp-170) cc_final: 0.6913 (ttp-170) REVERT: A 230 LEU cc_start: 0.8040 (mt) cc_final: 0.7768 (tp) REVERT: A 235 TYR cc_start: 0.7774 (m-80) cc_final: 0.7376 (m-80) REVERT: A 243 MET cc_start: 0.7491 (tpp) cc_final: 0.7166 (mmm) REVERT: A 268 ARG cc_start: 0.7185 (ptp-110) cc_final: 0.6912 (ptm160) outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 1.2923 time to fit residues: 80.3522 Evaluate side-chains 59 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.0050 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4429 Z= 0.203 Angle : 0.466 6.857 5997 Z= 0.233 Chirality : 0.038 0.130 710 Planarity : 0.004 0.035 732 Dihedral : 6.786 87.945 605 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.86 % Allowed : 14.66 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.36), residues: 543 helix: 2.45 (0.25), residues: 393 sheet: -1.17 (1.59), residues: 12 loop : -0.11 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE B 33 TYR 0.007 0.001 TYR A 137 ARG 0.004 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.513 Fit side-chains REVERT: B 34 GLN cc_start: 0.7188 (mt0) cc_final: 0.6840 (mt0) REVERT: C 86 MET cc_start: 0.7118 (mmp) cc_final: 0.6762 (mmm) REVERT: A 228 ARG cc_start: 0.7167 (ttp-170) cc_final: 0.6917 (ttp-170) REVERT: A 230 LEU cc_start: 0.8050 (mt) cc_final: 0.7784 (tp) REVERT: A 235 TYR cc_start: 0.7825 (m-80) cc_final: 0.7433 (m-80) REVERT: A 268 ARG cc_start: 0.7183 (ptp-110) cc_final: 0.6897 (ptm160) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 1.3826 time to fit residues: 84.5150 Evaluate side-chains 61 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 42 optimal weight: 9.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4429 Z= 0.165 Angle : 0.444 6.259 5997 Z= 0.222 Chirality : 0.037 0.129 710 Planarity : 0.004 0.035 732 Dihedral : 6.623 86.318 605 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.65 % Allowed : 14.87 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.36), residues: 543 helix: 2.59 (0.26), residues: 391 sheet: -1.25 (1.57), residues: 12 loop : -0.05 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.007 0.001 PHE A 112 TYR 0.007 0.001 TYR A 131 ARG 0.004 0.000 ARG A 311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.537 Fit side-chains REVERT: B 34 GLN cc_start: 0.7166 (mt0) cc_final: 0.6834 (mt0) REVERT: C 86 MET cc_start: 0.7097 (mmp) cc_final: 0.6747 (mmm) REVERT: A 228 ARG cc_start: 0.7168 (ttp-170) cc_final: 0.6915 (ttp-170) REVERT: A 230 LEU cc_start: 0.8037 (mt) cc_final: 0.7781 (tp) REVERT: A 235 TYR cc_start: 0.7766 (m-80) cc_final: 0.7363 (m-80) REVERT: A 243 MET cc_start: 0.7473 (tpp) cc_final: 0.7137 (mmm) REVERT: A 268 ARG cc_start: 0.7177 (ptp-110) cc_final: 0.6883 (ptm160) outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 1.3993 time to fit residues: 88.3702 Evaluate side-chains 61 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110780 restraints weight = 4641.194| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.86 r_work: 0.3323 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4429 Z= 0.183 Angle : 0.454 6.555 5997 Z= 0.228 Chirality : 0.037 0.129 710 Planarity : 0.004 0.035 732 Dihedral : 6.658 85.924 605 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.65 % Allowed : 15.09 % Favored : 84.27 % 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: 2.70 (0.36), residues: 543 helix: 2.50 (0.26), residues: 394 sheet: -1.30 (1.56), residues: 12 loop : -0.02 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.007 0.001 PHE A 112 TYR 0.007 0.001 TYR A 137 ARG 0.003 0.000 ARG A 311 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.15 seconds wall clock time: 38 minutes 36.74 seconds (2316.74 seconds total)