Starting phenix.real_space_refine on Fri Dec 27 11:27:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynj_33963/12_2024/7ynj_33963.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynj_33963/12_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/cci-nas-00/data/ceres_data/7ynj_33963/12_2024/7ynj_33963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynj_33963/12_2024/7ynj_33963.map" model { file = "/net/cci-nas-00/data/ceres_data/7ynj_33963/12_2024/7ynj_33963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynj_33963/12_2024/7ynj_33963.cif" } 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. Time to flip 4 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: 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: 3.82, per 1000 atoms: 0.87 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 - 3.00 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: 1.40 Conformation dependent library (CDL) restraints added in 732.8 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... Secondary structure from input PDB file: 32 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 26 through 46 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 112 removed outlier: 4.023A pdb=" N GLU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 4.266A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.723A pdb=" N TYR A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.314A pdb=" N ARG A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 173 through 192 Processing helix chain 'A' and resid 200 through 224 removed outlier: 3.630A pdb=" N HIS A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.937A pdb=" N ILE A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.590A pdb=" N VAL A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.957A pdb=" N THR A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 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 339 through 344 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 380 through 406 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 418 through 446 Proline residue: A 442 - end of helix removed outlier: 4.149A pdb=" N ALA A 446 " --> pdb=" O PRO A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 450 Processing helix chain 'A' and resid 451 through 477 removed outlier: 3.514A pdb=" N TYR A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) 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 481 through 507 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 518 through 523 Processing helix chain 'A' and resid 525 through 547 Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.050A pdb=" N ARG A 564 " --> pdb=" O PHE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 671 Processing helix chain 'B' and resid 29 through 55 320 hydrogen bonds defined for protein. 948 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: 1.24 Time building geometry restraints manager: 1.59 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: 0.00 - 2.18: 6017 2.18 - 4.36: 115 4.36 - 6.55: 11 6.55 - 8.73: 3 8.73 - 10.91: 1 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: 975 2.78 - 3.31: 4495 3.31 - 3.84: 7593 3.84 - 4.37: 8107 4.37 - 4.90: 14496 Nonbonded interactions: 35666 Sorted by model distance: nonbonded pdb=" O ILE A 501 " pdb=" OG SER A 505 " model vdw 2.249 3.040 nonbonded pdb=" O PHE A 561 " pdb=" NH1 ARG A 564 " model vdw 2.267 3.120 nonbonded pdb=" OH TYR A 128 " pdb=" O LEU A 559 " model vdw 2.286 3.040 nonbonded pdb=" O PHE A 220 " pdb=" N GLY A 225 " model vdw 2.303 3.120 nonbonded pdb=" O GLY A 86 " pdb=" OG SER A 362 " model vdw 2.351 3.040 ... (remaining 35661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.960 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.080 Process input model: 16.720 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- 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= 0.229 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 to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.410 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: 0.1321 time to fit residues: 15.3007 Evaluate side-chains 72 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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: 0.0970 chunk 24 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 52 optimal weight: 9.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.7031 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4491 Z= 0.221 Angle : 0.600 6.399 6147 Z= 0.307 Chirality : 0.043 0.158 733 Planarity : 0.005 0.048 748 Dihedral : 3.979 18.061 655 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.59 % Allowed : 8.02 % Favored : 89.39 % 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: 1.53 (0.36), residues: 582 helix: 1.61 (0.25), residues: 426 sheet: None (None), residues: 0 loop : -0.56 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 289 HIS 0.003 0.001 HIS A 80 PHE 0.026 0.002 PHE A 504 TYR 0.015 0.002 TYR A 339 ARG 0.005 0.001 ARG A 352 *********************** 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 to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 325 MET cc_start: 0.7089 (tmm) cc_final: 0.5826 (tmm) REVERT: A 535 PHE cc_start: 0.6691 (m-80) cc_final: 0.6476 (m-10) outliers start: 11 outliers final: 10 residues processed: 75 average time/residue: 0.1324 time to fit residues: 13.3760 Evaluate side-chains 78 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 203 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 536 CYS 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: 0.9980 chunk 16 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 0.0170 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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: 0.7078 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4491 Z= 0.226 Angle : 0.580 6.454 6147 Z= 0.300 Chirality : 0.042 0.145 733 Planarity : 0.005 0.047 748 Dihedral : 3.922 16.054 655 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.83 % Allowed : 13.44 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.36), residues: 582 helix: 1.46 (0.25), residues: 430 sheet: None (None), residues: 0 loop : -0.46 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 289 HIS 0.002 0.001 HIS A 80 PHE 0.021 0.001 PHE A 504 TYR 0.012 0.001 TYR A 339 ARG 0.003 0.001 ARG A 352 *********************** 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 85 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.514 Fit side-chains REVERT: A 325 MET cc_start: 0.7159 (tmm) cc_final: 0.5754 (tmm) outliers start: 12 outliers final: 10 residues processed: 77 average time/residue: 0.1316 time to fit residues: 13.5964 Evaluate side-chains 80 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 536 CYS Chi-restraints excluded: chain A residue 655 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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: 0.7253 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 4491 Z= 0.400 Angle : 0.698 6.884 6147 Z= 0.361 Chirality : 0.046 0.167 733 Planarity : 0.005 0.048 748 Dihedral : 4.378 17.724 655 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.48 % Allowed : 18.40 % Favored : 77.12 % 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: 0.87 (0.35), residues: 582 helix: 1.03 (0.24), residues: 423 sheet: None (None), residues: 0 loop : -0.46 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 429 HIS 0.003 0.001 HIS A 309 PHE 0.022 0.002 PHE A 504 TYR 0.017 0.002 TYR A 671 ARG 0.015 0.001 ARG A 352 *********************** 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 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.463 Fit side-chains REVERT: A 325 MET cc_start: 0.7605 (tmm) cc_final: 0.6013 (tmm) REVERT: A 394 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7386 (mp) outliers start: 19 outliers final: 14 residues processed: 81 average time/residue: 0.1406 time to fit residues: 15.0476 Evaluate side-chains 84 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 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 216 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 VAL 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: 0.5980 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7156 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4491 Z= 0.241 Angle : 0.596 6.390 6147 Z= 0.308 Chirality : 0.042 0.144 733 Planarity : 0.005 0.048 748 Dihedral : 4.034 18.246 655 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.72 % Allowed : 19.10 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.36), residues: 582 helix: 1.19 (0.25), residues: 426 sheet: None (None), residues: 0 loop : -0.43 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 289 HIS 0.004 0.001 HIS A 80 PHE 0.020 0.002 PHE A 504 TYR 0.013 0.001 TYR A 141 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 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.444 Fit side-chains REVERT: A 325 MET cc_start: 0.7408 (tmm) cc_final: 0.5998 (tmm) REVERT: A 448 GLN cc_start: 0.7698 (mm110) cc_final: 0.7476 (mm110) REVERT: A 655 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7048 (mm) outliers start: 20 outliers final: 14 residues processed: 86 average time/residue: 0.1309 time to fit residues: 15.1148 Evaluate side-chains 88 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 144 VAL 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 270 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 573 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.7209 moved from start: 0.2319 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= 0.287 Angle : 0.621 6.468 6147 Z= 0.320 Chirality : 0.043 0.152 733 Planarity : 0.005 0.048 748 Dihedral : 4.125 17.804 655 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.48 % Allowed : 20.05 % Favored : 75.47 % 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 (0.36), residues: 582 helix: 1.10 (0.25), residues: 426 sheet: None (None), residues: 0 loop : -0.47 (0.56), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 289 HIS 0.003 0.001 HIS A 80 PHE 0.019 0.002 PHE A 504 TYR 0.014 0.002 TYR A 671 ARG 0.004 0.001 ARG A 564 *********************** 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 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.492 Fit side-chains REVERT: A 325 MET cc_start: 0.7517 (tmm) cc_final: 0.6058 (tmm) REVERT: A 448 GLN cc_start: 0.7686 (mm110) cc_final: 0.7465 (mm110) REVERT: A 655 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7063 (mm) outliers start: 19 outliers final: 15 residues processed: 84 average time/residue: 0.1232 time to fit residues: 14.2767 Evaluate side-chains 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 144 VAL 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 444 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 573 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.0170 chunk 47 optimal weight: 0.0370 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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: 0.7082 moved from start: 0.2300 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= 0.189 Angle : 0.572 6.023 6147 Z= 0.293 Chirality : 0.041 0.133 733 Planarity : 0.005 0.050 748 Dihedral : 3.873 16.829 655 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.30 % Allowed : 21.93 % Favored : 74.76 % 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: 1.38 (0.36), residues: 582 helix: 1.46 (0.26), residues: 425 sheet: None (None), residues: 0 loop : -0.47 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 64 HIS 0.004 0.001 HIS A 80 PHE 0.017 0.001 PHE A 504 TYR 0.011 0.001 TYR A 671 ARG 0.004 0.000 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 91 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.520 Fit side-chains REVERT: A 655 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7063 (mm) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.1270 time to fit residues: 14.5008 Evaluate side-chains 84 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 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 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 53 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.0370 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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: 0.7122 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4491 Z= 0.231 Angle : 0.608 5.971 6147 Z= 0.313 Chirality : 0.042 0.145 733 Planarity : 0.005 0.051 748 Dihedral : 3.927 17.881 655 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.07 % Allowed : 23.58 % Favored : 73.35 % 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: 1.40 (0.36), residues: 582 helix: 1.49 (0.25), residues: 423 sheet: None (None), residues: 0 loop : -0.49 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 64 HIS 0.003 0.001 HIS A 80 PHE 0.022 0.001 PHE A 504 TYR 0.012 0.001 TYR A 141 ARG 0.005 0.001 ARG A 564 *********************** 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 84 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.457 Fit side-chains REVERT: A 655 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.7023 (mm) outliers start: 13 outliers final: 12 residues processed: 76 average time/residue: 0.1345 time to fit residues: 13.7796 Evaluate side-chains 83 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 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 536 CYS 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: 4.9990 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7170 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4491 Z= 0.269 Angle : 0.632 6.228 6147 Z= 0.325 Chirality : 0.043 0.151 733 Planarity : 0.005 0.050 748 Dihedral : 4.040 18.014 655 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.30 % Allowed : 23.58 % 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: 1.33 (0.36), residues: 582 helix: 1.41 (0.25), residues: 425 sheet: None (None), residues: 0 loop : -0.48 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 64 HIS 0.002 0.001 HIS A 80 PHE 0.021 0.002 PHE A 504 TYR 0.020 0.002 TYR A 671 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 84 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.480 Fit side-chains REVERT: A 655 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7039 (mm) outliers start: 14 outliers final: 12 residues processed: 76 average time/residue: 0.1357 time to fit residues: 14.3139 Evaluate side-chains 83 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 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 536 CYS 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 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4491 Z= 0.264 Angle : 0.625 6.879 6147 Z= 0.323 Chirality : 0.043 0.153 733 Planarity : 0.005 0.050 748 Dihedral : 4.045 18.154 655 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.01 % Allowed : 23.11 % Favored : 72.88 % 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: 1.29 (0.36), residues: 582 helix: 1.43 (0.25), residues: 423 sheet: None (None), residues: 0 loop : -0.59 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 64 HIS 0.003 0.001 HIS A 80 PHE 0.021 0.001 PHE A 504 TYR 0.012 0.001 TYR A 141 ARG 0.004 0.001 ARG A 564 ********************** 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 89 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.460 Fit side-chains REVERT: A 655 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7047 (mm) outliers start: 17 outliers final: 13 residues processed: 81 average time/residue: 0.1278 time to fit residues: 14.0815 Evaluate side-chains 82 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 157 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 444 VAL Chi-restraints excluded: chain A residue 536 CYS 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: 3.9990 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.175164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153829 restraints weight = 5219.789| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.23 r_work: 0.3759 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4491 Z= 0.246 Angle : 0.611 6.941 6147 Z= 0.316 Chirality : 0.043 0.182 733 Planarity : 0.005 0.050 748 Dihedral : 4.047 17.773 655 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.54 % Allowed : 23.82 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.36), residues: 582 helix: 1.47 (0.25), residues: 423 sheet: None (None), residues: 0 loop : -0.64 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 64 HIS 0.002 0.001 HIS A 80 PHE 0.021 0.001 PHE A 504 TYR 0.012 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: 1287.10 seconds wall clock time: 24 minutes 17.12 seconds (1457.12 seconds total)