Starting phenix.real_space_refine on Sat Dec 28 01:13:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b0n_15789/12_2024/8b0n_15789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0n_15789/12_2024/8b0n_15789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b0n_15789/12_2024/8b0n_15789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0n_15789/12_2024/8b0n_15789.map" model { file = "/net/cci-nas-00/data/ceres_data/8b0n_15789/12_2024/8b0n_15789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0n_15789/12_2024/8b0n_15789.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3852 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 15 5.16 5 C 2635 2.51 5 N 660 2.21 5 O 693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4004 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3972 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 36, 'TRANS': 473} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'OU9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.28, per 1000 atoms: 0.82 Number of scatterers: 4004 At special positions: 0 Unit cell: (59.472, 82.6, 85.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 1 15.00 O 693 8.00 N 660 7.00 C 2635 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 642.9 milliseconds 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 4 sheets defined 57.5% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 9 through 24 removed outlier: 3.560A pdb=" N GLY A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 34 through 47 removed outlier: 3.934A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 74 through 81 removed outlier: 3.653A pdb=" N SER A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 116 removed outlier: 4.257A pdb=" N TYR A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 126 through 140 removed outlier: 3.606A pdb=" N ALA A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.724A pdb=" N THR A 144 " --> pdb=" O TRP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 4.571A pdb=" N ASP A 157 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.645A pdb=" N ILE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 removed outlier: 4.053A pdb=" N LEU A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 218 through 221 Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.520A pdb=" N TRP A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 254 removed outlier: 4.389A pdb=" N LEU A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.569A pdb=" N LYS A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 4.318A pdb=" N SER A 349 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 419 through 437 removed outlier: 4.399A pdb=" N TRP A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 488 through 509 Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 273 removed outlier: 3.823A pdb=" N VAL A 300 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASP A 272 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA A 302 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 273 removed outlier: 3.823A pdb=" N VAL A 300 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASP A 272 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA A 302 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A 263 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLY A 298 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN A 223 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE A 264 " --> pdb=" O GLN A 223 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER A 225 " --> pdb=" O ILE A 264 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 376 removed outlier: 6.443A pdb=" N GLU A 381 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A 408 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR A 383 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE A 410 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA A 385 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 407 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N SER A 443 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 409 " --> pdb=" O SER A 443 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 573 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: 1.25 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 612 1.31 - 1.43: 1141 1.43 - 1.56: 2333 1.56 - 1.68: 1 1.68 - 1.80: 29 Bond restraints: 4116 Sorted by residual: bond pdb=" N P1L A 387 " pdb=" CA P1L A 387 " ideal model delta sigma weight residual 1.442 1.489 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C P1L A 387 " pdb=" O P1L A 387 " ideal model delta sigma weight residual 1.234 1.188 0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" O11 OU9 A 601 " pdb=" P OU9 A 601 " ideal model delta sigma weight residual 1.650 1.695 -0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" C11 OU9 A 601 " pdb=" O13 OU9 A 601 " ideal model delta sigma weight residual 1.418 1.375 0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" SG P1L A 387 " pdb=" C7 P1L A 387 " ideal model delta sigma weight residual 1.733 1.691 0.042 2.00e-02 2.50e+03 4.40e+00 ... (remaining 4111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 5517 1.77 - 3.54: 75 3.54 - 5.30: 18 5.30 - 7.07: 5 7.07 - 8.84: 2 Bond angle restraints: 5617 Sorted by residual: angle pdb=" SG P1L A 387 " pdb=" C7 P1L A 387 " pdb=" C8 P1L A 387 " ideal model delta sigma weight residual 109.23 118.07 -8.84 3.00e+00 1.11e-01 8.68e+00 angle pdb=" CA P1L A 387 " pdb=" C P1L A 387 " pdb=" O P1L A 387 " ideal model delta sigma weight residual 128.33 121.11 7.22 3.00e+00 1.11e-01 5.79e+00 angle pdb=" N GLY A 43 " pdb=" CA GLY A 43 " pdb=" C GLY A 43 " ideal model delta sigma weight residual 114.66 111.80 2.86 1.24e+00 6.50e-01 5.32e+00 angle pdb=" SG P1L A 387 " pdb=" C7 P1L A 387 " pdb=" O7 P1L A 387 " ideal model delta sigma weight residual 126.61 120.10 6.51 3.00e+00 1.11e-01 4.71e+00 angle pdb=" C2 OU9 A 601 " pdb=" C1 OU9 A 601 " pdb=" O11 OU9 A 601 " ideal model delta sigma weight residual 113.71 107.45 6.26 3.00e+00 1.11e-01 4.36e+00 ... (remaining 5612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 2284 15.57 - 31.14: 112 31.14 - 46.71: 17 46.71 - 62.28: 9 62.28 - 77.85: 4 Dihedral angle restraints: 2426 sinusoidal: 960 harmonic: 1466 Sorted by residual: dihedral pdb=" CA PHE A 28 " pdb=" C PHE A 28 " pdb=" N SER A 29 " pdb=" CA SER A 29 " ideal model delta harmonic sigma weight residual 180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CB GLU A 435 " pdb=" CG GLU A 435 " pdb=" CD GLU A 435 " pdb=" OE1 GLU A 435 " ideal model delta sinusoidal sigma weight residual 0.00 77.85 -77.85 1 3.00e+01 1.11e-03 8.42e+00 dihedral pdb=" CA TYR A 406 " pdb=" C TYR A 406 " pdb=" N LEU A 407 " pdb=" CA LEU A 407 " ideal model delta harmonic sigma weight residual 180.00 166.13 13.87 0 5.00e+00 4.00e-02 7.69e+00 ... (remaining 2423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 483 0.045 - 0.089: 101 0.089 - 0.134: 44 0.134 - 0.178: 2 0.178 - 0.223: 2 Chirality restraints: 632 Sorted by residual: chirality pdb=" CA P1L A 387 " pdb=" N P1L A 387 " pdb=" C P1L A 387 " pdb=" CB P1L A 387 " both_signs ideal model delta sigma weight residual False 2.27 2.49 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2 OU9 A 601 " pdb=" C1 OU9 A 601 " pdb=" C3 OU9 A 601 " pdb=" O21 OU9 A 601 " both_signs ideal model delta sigma weight residual False 2.54 2.73 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA TRP A 489 " pdb=" N TRP A 489 " pdb=" C TRP A 489 " pdb=" CB TRP A 489 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 629 not shown) Planarity restraints: 705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 87 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A 88 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 34 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO A 35 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 204 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 205 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.016 5.00e-02 4.00e+02 ... (remaining 702 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 964 2.79 - 3.32: 3989 3.32 - 3.85: 6977 3.85 - 4.37: 8714 4.37 - 4.90: 14571 Nonbonded interactions: 35215 Sorted by model distance: nonbonded pdb=" OH TYR A 333 " pdb=" OE1 GLU A 389 " model vdw 2.267 3.040 nonbonded pdb=" O PHE A 151 " pdb=" OG SER A 154 " model vdw 2.290 3.040 nonbonded pdb=" OG SER A 225 " pdb=" OG SER A 260 " model vdw 2.298 3.040 nonbonded pdb=" O GLY A 229 " pdb=" NH1 ARG A 467 " model vdw 2.300 3.120 nonbonded pdb=" O PRO A 361 " pdb=" N OU9 A 601 " model vdw 2.332 3.120 ... (remaining 35210 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.600 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 0.047 4116 Z= 0.224 Angle : 0.574 8.841 5617 Z= 0.256 Chirality : 0.044 0.223 632 Planarity : 0.004 0.037 705 Dihedral : 10.449 77.848 1486 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: 0.75 (0.38), residues: 505 helix: 1.01 (0.34), residues: 235 sheet: 0.49 (0.59), residues: 68 loop : 0.05 (0.48), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.008 0.001 PHE A 426 TYR 0.009 0.001 TYR A 406 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.481 Fit side-chains REVERT: A 8 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 11 ARG cc_start: 0.7302 (mmt180) cc_final: 0.6967 (mmt180) REVERT: A 304 LEU cc_start: 0.8244 (tp) cc_final: 0.7965 (tp) REVERT: A 310 TYR cc_start: 0.8544 (m-80) cc_final: 0.8283 (m-80) REVERT: A 428 MET cc_start: 0.8714 (mtt) cc_final: 0.8471 (mtp) REVERT: A 468 GLU cc_start: 0.8035 (tt0) cc_final: 0.7672 (tt0) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 1.0803 time to fit residues: 63.2531 Evaluate side-chains 47 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 24 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 244 ASN A 455 GLN A 488 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4116 Z= 0.178 Angle : 0.555 5.767 5617 Z= 0.277 Chirality : 0.043 0.168 632 Planarity : 0.005 0.036 705 Dihedral : 7.138 54.430 599 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.98 % Allowed : 4.90 % Favored : 94.12 % 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: 0.89 (0.38), residues: 505 helix: 1.25 (0.33), residues: 245 sheet: 0.27 (0.57), residues: 68 loop : -0.02 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.002 0.001 HIS A 337 PHE 0.012 0.001 PHE A 174 TYR 0.009 0.001 TYR A 406 ARG 0.007 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.415 Fit side-chains REVERT: A 8 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7469 (tm-30) REVERT: A 11 ARG cc_start: 0.7307 (mmt180) cc_final: 0.6961 (mmt180) REVERT: A 310 TYR cc_start: 0.8685 (m-80) cc_final: 0.8451 (m-80) REVERT: A 468 GLU cc_start: 0.8136 (tt0) cc_final: 0.7824 (tt0) outliers start: 4 outliers final: 1 residues processed: 50 average time/residue: 1.1236 time to fit residues: 58.5367 Evaluate side-chains 44 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.1980 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 244 ASN A 305 ASN A 314 ASN A 455 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4116 Z= 0.188 Angle : 0.537 5.861 5617 Z= 0.265 Chirality : 0.043 0.166 632 Planarity : 0.004 0.037 705 Dihedral : 6.639 49.750 599 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.47 % Allowed : 6.13 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.39), residues: 505 helix: 1.34 (0.33), residues: 251 sheet: 0.12 (0.57), residues: 67 loop : -0.01 (0.51), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.011 0.001 PHE A 174 TYR 0.009 0.001 TYR A 325 ARG 0.007 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.433 Fit side-chains REVERT: A 8 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 11 ARG cc_start: 0.7199 (mmt180) cc_final: 0.6814 (mmt180) REVERT: A 289 ARG cc_start: 0.6894 (mtm110) cc_final: 0.6658 (mtm110) REVERT: A 310 TYR cc_start: 0.8695 (m-80) cc_final: 0.8466 (m-80) outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 1.0727 time to fit residues: 56.0448 Evaluate side-chains 41 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 0.0570 chunk 5 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 244 ASN A 455 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4116 Z= 0.170 Angle : 0.530 5.786 5617 Z= 0.259 Chirality : 0.043 0.162 632 Planarity : 0.004 0.038 705 Dihedral : 6.233 50.373 599 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.98 % Allowed : 7.60 % Favored : 91.42 % 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: 1.02 (0.39), residues: 505 helix: 1.46 (0.33), residues: 251 sheet: 0.08 (0.56), residues: 67 loop : -0.05 (0.51), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.012 0.001 PHE A 174 TYR 0.008 0.001 TYR A 406 ARG 0.003 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.432 Fit side-chains REVERT: A 8 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 11 ARG cc_start: 0.7164 (mmt180) cc_final: 0.6781 (mmt180) REVERT: A 505 MET cc_start: 0.7929 (mmm) cc_final: 0.7639 (mmp) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 1.0678 time to fit residues: 46.9288 Evaluate side-chains 40 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4116 Z= 0.255 Angle : 0.551 5.946 5617 Z= 0.272 Chirality : 0.044 0.173 632 Planarity : 0.005 0.038 705 Dihedral : 6.447 57.764 599 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.23 % Allowed : 7.84 % Favored : 90.93 % 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 (0.38), residues: 505 helix: 1.39 (0.33), residues: 250 sheet: 0.29 (0.56), residues: 63 loop : -0.07 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.013 0.001 PHE A 174 TYR 0.010 0.001 TYR A 325 ARG 0.010 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.450 Fit side-chains REVERT: A 8 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 11 ARG cc_start: 0.7201 (mmt180) cc_final: 0.6820 (mmt180) REVERT: A 289 ARG cc_start: 0.6951 (mtm110) cc_final: 0.6711 (mtm110) REVERT: A 505 MET cc_start: 0.7901 (mmm) cc_final: 0.7592 (mmp) outliers start: 5 outliers final: 2 residues processed: 41 average time/residue: 1.0855 time to fit residues: 46.5677 Evaluate side-chains 40 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4116 Z= 0.242 Angle : 0.556 5.941 5617 Z= 0.275 Chirality : 0.044 0.170 632 Planarity : 0.004 0.038 705 Dihedral : 6.420 59.465 599 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.98 % Allowed : 8.09 % Favored : 90.93 % 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: 0.96 (0.38), residues: 505 helix: 1.40 (0.33), residues: 250 sheet: 0.26 (0.56), residues: 63 loop : -0.13 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.013 0.001 PHE A 174 TYR 0.010 0.001 TYR A 325 ARG 0.006 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.476 Fit side-chains REVERT: A 11 ARG cc_start: 0.7199 (mmt180) cc_final: 0.6820 (mmt180) REVERT: A 505 MET cc_start: 0.7887 (mmm) cc_final: 0.7592 (mmp) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 1.0149 time to fit residues: 44.7748 Evaluate side-chains 39 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.0770 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 241 GLN A 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4116 Z= 0.192 Angle : 0.544 5.839 5617 Z= 0.269 Chirality : 0.043 0.162 632 Planarity : 0.005 0.041 705 Dihedral : 6.257 59.902 599 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.98 % Allowed : 8.33 % Favored : 90.69 % 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: 0.93 (0.38), residues: 505 helix: 1.44 (0.33), residues: 252 sheet: -0.04 (0.56), residues: 67 loop : -0.16 (0.50), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.013 0.001 PHE A 174 TYR 0.009 0.001 TYR A 325 ARG 0.013 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.469 Fit side-chains REVERT: A 11 ARG cc_start: 0.7163 (mmt180) cc_final: 0.6801 (mmt180) REVERT: A 289 ARG cc_start: 0.6952 (mtm110) cc_final: 0.6720 (mtm110) REVERT: A 505 MET cc_start: 0.7836 (mmm) cc_final: 0.7558 (mmp) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 1.0601 time to fit residues: 46.8216 Evaluate side-chains 39 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.0570 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 14 optimal weight: 0.5980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4116 Z= 0.156 Angle : 0.525 5.763 5617 Z= 0.257 Chirality : 0.043 0.164 632 Planarity : 0.004 0.041 705 Dihedral : 6.013 59.905 599 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.74 % Allowed : 9.31 % Favored : 89.95 % 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 (0.39), residues: 505 helix: 1.59 (0.33), residues: 253 sheet: -0.02 (0.56), residues: 67 loop : -0.11 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.011 0.001 PHE A 174 TYR 0.009 0.001 TYR A 406 ARG 0.010 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.473 Fit side-chains REVERT: A 11 ARG cc_start: 0.7206 (mmt180) cc_final: 0.6832 (mmt180) REVERT: A 505 MET cc_start: 0.7814 (mmm) cc_final: 0.7558 (mmp) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 1.1251 time to fit residues: 46.0038 Evaluate side-chains 40 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4116 Z= 0.212 Angle : 0.543 5.849 5617 Z= 0.268 Chirality : 0.044 0.169 632 Planarity : 0.005 0.050 705 Dihedral : 6.121 58.798 599 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.74 % Allowed : 9.80 % Favored : 89.46 % 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: 0.97 (0.39), residues: 505 helix: 1.48 (0.33), residues: 253 sheet: -0.03 (0.56), residues: 67 loop : -0.16 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.012 0.001 PHE A 174 TYR 0.009 0.001 TYR A 325 ARG 0.014 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.333 Fit side-chains REVERT: A 11 ARG cc_start: 0.7215 (mmt180) cc_final: 0.6836 (mmt180) REVERT: A 247 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7394 (ttpt) REVERT: A 505 MET cc_start: 0.7857 (mmm) cc_final: 0.7579 (mmp) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 1.0455 time to fit residues: 43.7130 Evaluate side-chains 41 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.0470 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 0.002 0.026 4116 Z= 0.147 Angle : 0.519 5.724 5617 Z= 0.254 Chirality : 0.042 0.163 632 Planarity : 0.004 0.048 705 Dihedral : 5.906 59.160 599 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.74 % Allowed : 9.80 % Favored : 89.46 % 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: 1.12 (0.39), residues: 505 helix: 1.61 (0.33), residues: 254 sheet: -0.01 (0.57), residues: 67 loop : -0.08 (0.51), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.012 0.001 PHE A 174 TYR 0.008 0.001 TYR A 406 ARG 0.010 0.000 ARG A 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.450 Fit side-chains REVERT: A 11 ARG cc_start: 0.7209 (mmt180) cc_final: 0.6873 (mmt180) REVERT: A 247 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7415 (ttpt) REVERT: A 485 ARG cc_start: 0.7581 (mtt-85) cc_final: 0.7370 (mtt90) REVERT: A 505 MET cc_start: 0.7792 (mmm) cc_final: 0.7551 (mmp) outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 1.2655 time to fit residues: 59.1159 Evaluate side-chains 47 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.087006 restraints weight = 4637.465| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.00 r_work: 0.2796 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4116 Z= 0.213 Angle : 0.544 5.847 5617 Z= 0.267 Chirality : 0.044 0.170 632 Planarity : 0.004 0.038 705 Dihedral : 6.050 58.241 599 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.98 % Allowed : 10.05 % Favored : 88.97 % 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: 1.03 (0.39), residues: 505 helix: 1.52 (0.33), residues: 253 sheet: 0.01 (0.57), residues: 67 loop : -0.11 (0.51), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.013 0.001 PHE A 174 TYR 0.010 0.001 TYR A 325 ARG 0.005 0.000 ARG A 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1733.75 seconds wall clock time: 35 minutes 51.52 seconds (2151.52 seconds total)