Starting phenix.real_space_refine on Tue Feb 13 08:13:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynj_33963/02_2024/7ynj_33963_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynj_33963/02_2024/7ynj_33963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynj_33963/02_2024/7ynj_33963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynj_33963/02_2024/7ynj_33963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynj_33963/02_2024/7ynj_33963_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynj_33963/02_2024/7ynj_33963_updated.pdb" } resolution = 3.33 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= 0.075 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 33 5.16 5 C 2905 2.51 5 N 712 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 4371 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4145 Classifications: {'peptide': 564} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 26, 'TRANS': 537} Chain breaks: 3 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 121 Chain: "B" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 26} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'GYP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.66, per 1000 atoms: 0.61 Number of scatterers: 4371 At special positions: 0 Unit cell: (74.711, 64.859, 88.668, 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 33 16.00 O 721 8.00 N 712 7.00 C 2905 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 785.8 milliseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1078 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 0 sheets defined 71.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 27 through 45 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 93 through 111 removed outlier: 3.664A pdb=" N TRP A 100 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 104 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 119 Processing helix chain 'A' and resid 125 through 132 removed outlier: 3.562A pdb=" N LEU A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.549A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 174 through 191 Processing helix chain 'A' and resid 200 through 223 removed outlier: 3.630A pdb=" N HIS A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 282 through 291 removed outlier: 4.037A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 307 through 338 removed outlier: 3.957A pdb=" N THR A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 4.309A pdb=" N MET A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 419 through 445 Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 452 through 476 removed outlier: 3.530A pdb=" N TYR A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 482 through 506 removed outlier: 3.686A pdb=" N GLY A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Proline residue: A 502 - end of helix Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 519 through 522 No H-bonds generated for 'chain 'A' and resid 519 through 522' Processing helix chain 'A' and resid 526 through 546 Processing helix chain 'A' and resid 553 through 555 No H-bonds generated for 'chain 'A' and resid 553 through 555' Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 647 through 670 Processing helix chain 'B' and resid 29 through 54 279 hydrogen bonds defined for protein. 798 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: 1.16 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1318 1.34 - 1.46: 1174 1.46 - 1.58: 1950 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 4491 Sorted by residual: bond pdb=" C1 GYP A 701 " pdb=" O1 GYP A 701 " ideal model delta sigma weight residual 1.387 1.426 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C TYR A 366 " pdb=" N PRO A 367 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.30e-02 5.92e+03 3.48e+00 bond pdb=" C1 GYP A 701 " pdb=" O5 GYP A 701 " ideal model delta sigma weight residual 1.400 1.431 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C2 GYP A 701 " pdb=" O2 GYP A 701 " ideal model delta sigma weight residual 1.402 1.430 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C6 GYP A 701 " pdb=" O6 GYP A 701 " ideal model delta sigma weight residual 1.407 1.432 -0.025 2.00e-02 2.50e+03 1.56e+00 ... (remaining 4486 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.65: 99 105.65 - 112.74: 2417 112.74 - 119.82: 1413 119.82 - 126.90: 2135 126.90 - 133.99: 83 Bond angle restraints: 6147 Sorted by residual: angle pdb=" C LEU A 322 " pdb=" N THR A 323 " pdb=" CA THR A 323 " ideal model delta sigma weight residual 120.09 131.00 -10.91 1.25e+00 6.40e-01 7.62e+01 angle pdb=" N VAL A 346 " pdb=" CA VAL A 346 " pdb=" C VAL A 346 " ideal model delta sigma weight residual 113.71 109.69 4.02 9.50e-01 1.11e+00 1.79e+01 angle pdb=" N VAL A 248 " pdb=" CA VAL A 248 " pdb=" C VAL A 248 " ideal model delta sigma weight residual 113.53 109.83 3.70 9.80e-01 1.04e+00 1.43e+01 angle pdb=" N THR A 323 " pdb=" CA THR A 323 " pdb=" C THR A 323 " ideal model delta sigma weight residual 113.16 116.81 -3.65 1.42e+00 4.96e-01 6.62e+00 angle pdb=" C THR A 548 " pdb=" N ALA A 549 " pdb=" CA ALA A 549 " ideal model delta sigma weight residual 120.65 123.82 -3.17 1.36e+00 5.41e-01 5.44e+00 ... (remaining 6142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 2361 17.54 - 35.08: 163 35.08 - 52.62: 42 52.62 - 70.16: 3 70.16 - 87.70: 3 Dihedral angle restraints: 2572 sinusoidal: 884 harmonic: 1688 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -154.35 68.35 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CB CYS A 255 " pdb=" SG CYS A 255 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual 93.00 156.87 -63.87 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 145.25 -52.25 1 1.00e+01 1.00e-02 3.72e+01 ... (remaining 2569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 518 0.045 - 0.089: 183 0.089 - 0.134: 28 0.134 - 0.178: 3 0.178 - 0.223: 1 Chirality restraints: 733 Sorted by residual: chirality pdb=" CG LEU A 322 " pdb=" CB LEU A 322 " pdb=" CD1 LEU A 322 " pdb=" CD2 LEU A 322 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA PHE A 152 " pdb=" N PHE A 152 " pdb=" C PHE A 152 " pdb=" CB PHE A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA TRP A 65 " pdb=" N TRP A 65 " pdb=" C TRP A 65 " pdb=" CB TRP A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 730 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 465 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 466 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 279 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C LEU A 279 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU A 279 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 280 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 501 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 502 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.028 5.00e-02 4.00e+02 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 989 2.78 - 3.31: 4524 3.31 - 3.84: 7638 3.84 - 4.37: 8171 4.37 - 4.90: 14508 Nonbonded interactions: 35830 Sorted by model distance: nonbonded pdb=" O ILE A 501 " pdb=" OG SER A 505 " model vdw 2.249 2.440 nonbonded pdb=" O PHE A 561 " pdb=" NH1 ARG A 564 " model vdw 2.267 2.520 nonbonded pdb=" OH TYR A 128 " pdb=" O LEU A 559 " model vdw 2.286 2.440 nonbonded pdb=" O PHE A 220 " pdb=" N GLY A 225 " model vdw 2.303 2.520 nonbonded pdb=" O GLY A 86 " pdb=" OG SER A 362 " model vdw 2.351 2.440 ... (remaining 35825 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: 0.900 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: 4.560 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.420 Find NCS groups from input model: 0.140 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 : 0.004 0.046 4491 Z= 0.239 Angle : 0.679 10.909 6147 Z= 0.366 Chirality : 0.043 0.223 733 Planarity : 0.005 0.054 748 Dihedral : 12.776 87.697 1482 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.35), residues: 582 helix: 1.67 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -0.94 (0.48), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.002 0.001 HIS A 555 PHE 0.012 0.001 PHE A 113 TYR 0.011 0.001 TYR A 128 ARG 0.007 0.001 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.477 Fit side-chains REVERT: A 325 MET cc_start: 0.6917 (tmm) cc_final: 0.5623 (tmm) REVERT: A 535 PHE cc_start: 0.6590 (m-80) cc_final: 0.6311 (m-10) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1320 time to fit residues: 15.4175 Evaluate side-chains 72 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 24 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.0040 overall best weight: 0.2550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4491 Z= 0.198 Angle : 0.561 6.412 6147 Z= 0.281 Chirality : 0.041 0.175 733 Planarity : 0.005 0.049 748 Dihedral : 3.873 21.822 655 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.89 % Allowed : 8.96 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.36), residues: 582 helix: 1.85 (0.26), residues: 418 sheet: None (None), residues: 0 loop : -0.81 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 65 HIS 0.002 0.001 HIS A 555 PHE 0.025 0.001 PHE A 504 TYR 0.012 0.001 TYR A 175 ARG 0.005 0.001 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.476 Fit side-chains REVERT: A 325 MET cc_start: 0.7020 (tmm) cc_final: 0.5833 (tmm) REVERT: A 535 PHE cc_start: 0.6649 (m-80) cc_final: 0.6442 (m-10) outliers start: 8 outliers final: 7 residues processed: 75 average time/residue: 0.1286 time to fit residues: 13.0329 Evaluate side-chains 78 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 655 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 43 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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: 0.7039 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4491 Z= 0.205 Angle : 0.542 6.417 6147 Z= 0.274 Chirality : 0.041 0.143 733 Planarity : 0.005 0.047 748 Dihedral : 3.782 20.512 655 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.59 % Allowed : 12.26 % Favored : 85.14 % 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: 1.60 (0.36), residues: 582 helix: 1.71 (0.26), residues: 425 sheet: None (None), residues: 0 loop : -0.69 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 289 HIS 0.002 0.001 HIS A 555 PHE 0.020 0.001 PHE A 504 TYR 0.010 0.001 TYR A 141 ARG 0.003 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.523 Fit side-chains REVERT: A 325 MET cc_start: 0.7208 (tmm) cc_final: 0.5858 (tmm) outliers start: 11 outliers final: 7 residues processed: 73 average time/residue: 0.1406 time to fit residues: 13.6886 Evaluate side-chains 75 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 4491 Z= 0.559 Angle : 0.819 8.914 6147 Z= 0.419 Chirality : 0.052 0.234 733 Planarity : 0.006 0.050 748 Dihedral : 4.883 19.503 655 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.48 % Allowed : 17.45 % Favored : 78.07 % 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: 0.29 (0.35), residues: 582 helix: 0.66 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.78 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 429 HIS 0.005 0.002 HIS A 80 PHE 0.025 0.003 PHE A 504 TYR 0.022 0.003 TYR A 226 ARG 0.006 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.481 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 86 average time/residue: 0.1436 time to fit residues: 16.1940 Evaluate side-chains 86 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 0.0050 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4491 Z= 0.225 Angle : 0.599 9.535 6147 Z= 0.301 Chirality : 0.042 0.219 733 Planarity : 0.005 0.048 748 Dihedral : 3.990 15.019 655 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.01 % Allowed : 20.28 % Favored : 75.71 % 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 (0.36), residues: 582 helix: 1.22 (0.25), residues: 419 sheet: None (None), residues: 0 loop : -0.70 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 289 HIS 0.003 0.001 HIS A 555 PHE 0.026 0.001 PHE A 81 TYR 0.013 0.001 TYR A 339 ARG 0.007 0.001 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.483 Fit side-chains REVERT: A 151 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7511 (mp) REVERT: A 535 PHE cc_start: 0.6856 (m-10) cc_final: 0.6602 (m-10) outliers start: 17 outliers final: 9 residues processed: 90 average time/residue: 0.1308 time to fit residues: 15.6548 Evaluate side-chains 86 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.0070 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 overall best weight: 0.2998 ------------------------------------------------------------------------------- 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: 0.7093 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4491 Z= 0.189 Angle : 0.567 8.482 6147 Z= 0.283 Chirality : 0.041 0.167 733 Planarity : 0.005 0.047 748 Dihedral : 3.718 13.520 655 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.54 % Allowed : 21.23 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.36), residues: 582 helix: 1.48 (0.26), residues: 418 sheet: None (None), residues: 0 loop : -0.84 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 289 HIS 0.002 0.001 HIS A 555 PHE 0.028 0.001 PHE A 504 TYR 0.015 0.001 TYR A 175 ARG 0.004 0.001 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.471 Fit side-chains REVERT: A 151 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7466 (mp) REVERT: A 533 LEU cc_start: 0.8305 (tt) cc_final: 0.8094 (tp) REVERT: A 535 PHE cc_start: 0.6715 (m-10) cc_final: 0.6443 (m-10) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.1345 time to fit residues: 16.1645 Evaluate side-chains 89 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.0370 chunk 47 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4491 Z= 0.250 Angle : 0.615 8.832 6147 Z= 0.306 Chirality : 0.042 0.173 733 Planarity : 0.005 0.047 748 Dihedral : 3.836 14.152 655 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.25 % Allowed : 21.70 % Favored : 74.06 % 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: 1.18 (0.36), residues: 582 helix: 1.44 (0.26), residues: 418 sheet: None (None), residues: 0 loop : -0.87 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 64 HIS 0.002 0.001 HIS A 555 PHE 0.024 0.001 PHE A 504 TYR 0.013 0.002 TYR A 233 ARG 0.003 0.001 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.488 Fit side-chains REVERT: A 151 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7496 (mp) REVERT: A 535 PHE cc_start: 0.6826 (m-10) cc_final: 0.6531 (m-10) outliers start: 18 outliers final: 14 residues processed: 83 average time/residue: 0.1330 time to fit residues: 14.9399 Evaluate side-chains 90 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 50 optimal weight: 0.0030 chunk 53 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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: 0.7147 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4491 Z= 0.234 Angle : 0.610 8.627 6147 Z= 0.303 Chirality : 0.042 0.173 733 Planarity : 0.005 0.050 748 Dihedral : 3.813 14.207 655 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.95 % Allowed : 21.23 % Favored : 73.82 % 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: 1.23 (0.36), residues: 582 helix: 1.46 (0.26), residues: 418 sheet: None (None), residues: 0 loop : -0.82 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 64 HIS 0.002 0.001 HIS A 555 PHE 0.024 0.001 PHE A 504 TYR 0.011 0.001 TYR A 141 ARG 0.006 0.001 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.474 Fit side-chains REVERT: A 151 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7482 (mp) REVERT: A 535 PHE cc_start: 0.6811 (m-10) cc_final: 0.6503 (m-10) outliers start: 21 outliers final: 18 residues processed: 87 average time/residue: 0.1417 time to fit residues: 16.2846 Evaluate side-chains 92 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4491 Z= 0.271 Angle : 0.641 8.716 6147 Z= 0.321 Chirality : 0.043 0.177 733 Planarity : 0.005 0.051 748 Dihedral : 3.962 15.433 655 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.42 % Allowed : 21.46 % Favored : 73.11 % 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: 1.08 (0.36), residues: 582 helix: 1.30 (0.25), residues: 420 sheet: None (None), residues: 0 loop : -0.73 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 64 HIS 0.002 0.001 HIS A 555 PHE 0.024 0.002 PHE A 504 TYR 0.013 0.002 TYR A 141 ARG 0.004 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 0.473 Fit side-chains REVERT: A 151 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7486 (mp) REVERT: A 661 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6193 (tpp) outliers start: 23 outliers final: 18 residues processed: 87 average time/residue: 0.1261 time to fit residues: 14.8191 Evaluate side-chains 94 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 36 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 6 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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: 0.7077 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4491 Z= 0.203 Angle : 0.618 8.410 6147 Z= 0.303 Chirality : 0.041 0.168 733 Planarity : 0.005 0.052 748 Dihedral : 3.759 15.099 655 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.83 % Allowed : 24.06 % Favored : 73.11 % 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: 1.30 (0.36), residues: 582 helix: 1.49 (0.26), residues: 419 sheet: None (None), residues: 0 loop : -0.71 (0.51), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 64 HIS 0.002 0.001 HIS A 555 PHE 0.022 0.001 PHE A 504 TYR 0.009 0.001 TYR A 141 ARG 0.005 0.001 ARG A 352 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 151 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7489 (mp) REVERT: A 535 PHE cc_start: 0.6707 (m-10) cc_final: 0.6439 (m-10) outliers start: 12 outliers final: 11 residues processed: 80 average time/residue: 0.1349 time to fit residues: 14.4855 Evaluate side-chains 86 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.0040 chunk 40 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 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 = 0.4092 r_free = 0.4092 target = 0.175371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.154293 restraints weight = 5363.989| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.32 r_work: 0.3774 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4491 Z= 0.232 Angle : 0.623 8.535 6147 Z= 0.308 Chirality : 0.042 0.165 733 Planarity : 0.005 0.053 748 Dihedral : 3.845 16.991 655 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.07 % Allowed : 22.88 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.36), residues: 582 helix: 1.47 (0.26), residues: 418 sheet: None (None), residues: 0 loop : -0.74 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 64 HIS 0.002 0.001 HIS A 555 PHE 0.025 0.001 PHE A 504 TYR 0.011 0.001 TYR A 141 ARG 0.004 0.001 ARG A 564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1316.92 seconds wall clock time: 24 minutes 23.37 seconds (1463.37 seconds total)