Starting phenix.real_space_refine on Wed Jun 4 22:15:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kr7_62521/06_2025/9kr7_62521.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kr7_62521/06_2025/9kr7_62521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kr7_62521/06_2025/9kr7_62521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kr7_62521/06_2025/9kr7_62521.map" model { file = "/net/cci-nas-00/data/ceres_data/9kr7_62521/06_2025/9kr7_62521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kr7_62521/06_2025/9kr7_62521.cif" } resolution = 3.29 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 37 5.16 5 Cl 1 4.86 5 C 2858 2.51 5 N 658 2.21 5 O 707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4261 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4253 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 1 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1, 'water': 7} Link IDs: {None: 7} Time building chain proxies: 3.97, per 1000 atoms: 0.93 Number of scatterers: 4261 At special positions: 0 Unit cell: (84.4, 68.575, 88.62, 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) Cl 1 17.00 S 37 16.00 O 707 8.00 N 658 7.00 C 2858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 181 " 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 531.4 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 80.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 57 through 70 removed outlier: 4.410A pdb=" N PHE A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.555A pdb=" N VAL A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 86 through 101 removed outlier: 3.514A pdb=" N PHE A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 101 through 117 Processing helix chain 'A' and resid 121 through 130 removed outlier: 3.863A pdb=" N ILE A 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 131 through 163 removed outlier: 3.595A pdb=" N TYR A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N MET A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.924A pdb=" N THR A 171 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.548A pdb=" N CYS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 281 removed outlier: 3.574A pdb=" N THR A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 284 through 294 removed outlier: 3.622A pdb=" N GLY A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 302 through 317 removed outlier: 4.240A pdb=" N TRP A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.620A pdb=" N ALA A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 371 removed outlier: 3.656A pdb=" N ILE A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.517A pdb=" N VAL A 377 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 394 removed outlier: 3.531A pdb=" N ARG A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 433 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 465 through 476 removed outlier: 4.224A pdb=" N VAL A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.525A pdb=" N LEU A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 516 through 525 removed outlier: 4.161A pdb=" N LYS A 520 " --> pdb=" O CYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 554 through 570 Processing helix chain 'A' and resid 570 through 583 Processing helix chain 'A' and resid 586 through 595 Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 283 hydrogen bonds defined for protein. 822 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: 1.43 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1236 1.34 - 1.46: 1176 1.46 - 1.58: 1934 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 4400 Sorted by residual: bond pdb=" N ASN A 85 " pdb=" CA ASN A 85 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.75e+00 bond pdb=" N TYR A 80 " pdb=" CA TYR A 80 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.63e+00 bond pdb=" N VAL A 75 " pdb=" CA VAL A 75 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.34e-02 5.57e+03 6.52e+00 bond pdb=" N ARG A 77 " pdb=" CA ARG A 77 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.28e+00 bond pdb=" N TYR A 83 " pdb=" CA TYR A 83 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.22e+00 ... (remaining 4395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 5785 1.28 - 2.57: 170 2.57 - 3.85: 42 3.85 - 5.13: 9 5.13 - 6.41: 4 Bond angle restraints: 6010 Sorted by residual: angle pdb=" CA ARG A 77 " pdb=" C ARG A 77 " pdb=" O ARG A 77 " ideal model delta sigma weight residual 120.70 117.82 2.88 1.03e+00 9.43e-01 7.82e+00 angle pdb=" N LEU A 72 " pdb=" CA LEU A 72 " pdb=" C LEU A 72 " ideal model delta sigma weight residual 112.89 109.46 3.43 1.24e+00 6.50e-01 7.66e+00 angle pdb=" CA CYS A 82 " pdb=" C CYS A 82 " pdb=" O CYS A 82 " ideal model delta sigma weight residual 120.82 118.03 2.79 1.05e+00 9.07e-01 7.08e+00 angle pdb=" N GLY A 73 " pdb=" CA GLY A 73 " pdb=" C GLY A 73 " ideal model delta sigma weight residual 114.16 111.05 3.11 1.21e+00 6.83e-01 6.62e+00 angle pdb=" C TYR A 80 " pdb=" CA TYR A 80 " pdb=" CB TYR A 80 " ideal model delta sigma weight residual 110.88 114.84 -3.96 1.57e+00 4.06e-01 6.37e+00 ... (remaining 6005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2230 17.67 - 35.33: 187 35.33 - 53.00: 23 53.00 - 70.66: 6 70.66 - 88.33: 3 Dihedral angle restraints: 2449 sinusoidal: 915 harmonic: 1534 Sorted by residual: dihedral pdb=" CD ARG A 77 " pdb=" NE ARG A 77 " pdb=" CZ ARG A 77 " pdb=" NH1 ARG A 77 " ideal model delta sinusoidal sigma weight residual 0.00 -29.22 29.22 1 1.00e+01 1.00e-02 1.22e+01 dihedral pdb=" CB GLU A 423 " pdb=" CG GLU A 423 " pdb=" CD GLU A 423 " pdb=" OE1 GLU A 423 " ideal model delta sinusoidal sigma weight residual 0.00 88.33 -88.33 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU A 558 " pdb=" CG GLU A 558 " pdb=" CD GLU A 558 " pdb=" OE1 GLU A 558 " ideal model delta sinusoidal sigma weight residual 0.00 -86.37 86.37 1 3.00e+01 1.11e-03 9.99e+00 ... (remaining 2446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 450 0.038 - 0.076: 161 0.076 - 0.114: 39 0.114 - 0.152: 6 0.152 - 0.190: 1 Chirality restraints: 657 Sorted by residual: chirality pdb=" CA VAL A 75 " pdb=" N VAL A 75 " pdb=" C VAL A 75 " pdb=" CB VAL A 75 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA ASN A 74 " pdb=" N ASN A 74 " pdb=" C ASN A 74 " pdb=" CB ASN A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA THR A 527 " pdb=" N THR A 527 " pdb=" C THR A 527 " pdb=" CB THR A 527 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 654 not shown) Planarity restraints: 730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 77 " -0.525 9.50e-02 1.11e+02 2.36e-01 3.40e+01 pdb=" NE ARG A 77 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 77 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 77 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 77 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 151 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C VAL A 151 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL A 151 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 152 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 381 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 382 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " 0.020 5.00e-02 4.00e+02 ... (remaining 727 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 342 2.74 - 3.28: 4525 3.28 - 3.82: 7401 3.82 - 4.36: 8578 4.36 - 4.90: 14993 Nonbonded interactions: 35839 Sorted by model distance: nonbonded pdb=" OD1 ASP A 60 " pdb=" OH TYR A 262 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR A 586 " pdb=" OE1 GLU A 589 " model vdw 2.213 3.040 nonbonded pdb=" O ASN A 232 " pdb=" OG1 THR A 236 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A 269 " pdb=" OG1 THR A 351 " model vdw 2.270 3.040 nonbonded pdb=" O SER A 316 " pdb=" O HOH A 801 " model vdw 2.282 3.040 ... (remaining 35834 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: 0.770 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.400 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: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 0.044 4401 Z= 0.227 Angle : 0.566 6.414 6012 Z= 0.321 Chirality : 0.040 0.190 657 Planarity : 0.010 0.236 730 Dihedral : 13.528 88.330 1474 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.22 % Allowed : 0.67 % Favored : 99.10 % 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: 0.41 (0.37), residues: 530 helix: 0.71 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.54 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 555 HIS 0.002 0.001 HIS A 603 PHE 0.012 0.001 PHE A 106 TYR 0.013 0.001 TYR A 80 ARG 0.002 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.15335 ( 283) hydrogen bonds : angle 6.82725 ( 822) SS BOND : bond 0.00230 ( 1) SS BOND : angle 0.72574 ( 2) covalent geometry : bond 0.00439 ( 4400) covalent geometry : angle 0.56555 ( 6010) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.479 Fit side-chains REVERT: A 464 ASP cc_start: 0.8812 (m-30) cc_final: 0.8550 (m-30) outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.1376 time to fit residues: 14.2064 Evaluate side-chains 66 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.129257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.107618 restraints weight = 5452.879| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.51 r_work: 0.3016 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4401 Z= 0.159 Angle : 0.534 5.580 6012 Z= 0.275 Chirality : 0.039 0.134 657 Planarity : 0.004 0.038 730 Dihedral : 4.402 50.397 579 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.57 % Allowed : 6.73 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.38), residues: 530 helix: 1.52 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.34 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 76 HIS 0.002 0.001 HIS A 603 PHE 0.016 0.001 PHE A 115 TYR 0.018 0.001 TYR A 148 ARG 0.002 0.000 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 283) hydrogen bonds : angle 4.44106 ( 822) SS BOND : bond 0.00408 ( 1) SS BOND : angle 1.38696 ( 2) covalent geometry : bond 0.00372 ( 4400) covalent geometry : angle 0.53386 ( 6010) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.471 Fit side-chains REVERT: A 115 PHE cc_start: 0.8860 (t80) cc_final: 0.8643 (t80) REVERT: A 464 ASP cc_start: 0.8705 (m-30) cc_final: 0.8443 (m-30) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.1283 time to fit residues: 12.7255 Evaluate side-chains 70 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.129766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.107742 restraints weight = 5478.006| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.54 r_work: 0.2984 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4401 Z= 0.165 Angle : 0.534 5.627 6012 Z= 0.273 Chirality : 0.039 0.131 657 Planarity : 0.004 0.036 730 Dihedral : 4.404 51.957 579 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.47 % Allowed : 7.62 % Favored : 89.91 % 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: 1.57 (0.38), residues: 530 helix: 1.63 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.33 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 485 HIS 0.002 0.001 HIS A 603 PHE 0.013 0.001 PHE A 115 TYR 0.016 0.001 TYR A 80 ARG 0.001 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 283) hydrogen bonds : angle 4.28014 ( 822) SS BOND : bond 0.00316 ( 1) SS BOND : angle 1.23447 ( 2) covalent geometry : bond 0.00395 ( 4400) covalent geometry : angle 0.53360 ( 6010) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.463 Fit side-chains REVERT: A 115 PHE cc_start: 0.8840 (t80) cc_final: 0.8613 (t80) REVERT: A 357 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7619 (t80) REVERT: A 464 ASP cc_start: 0.8768 (m-30) cc_final: 0.8454 (m-30) outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 0.1367 time to fit residues: 12.8991 Evaluate side-chains 74 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.130083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.108075 restraints weight = 5461.682| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.55 r_work: 0.2996 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4401 Z= 0.138 Angle : 0.515 7.226 6012 Z= 0.259 Chirality : 0.038 0.126 657 Planarity : 0.004 0.035 730 Dihedral : 4.348 53.758 579 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.47 % Allowed : 9.42 % Favored : 88.12 % 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: 1.70 (0.38), residues: 530 helix: 1.76 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.36 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 485 HIS 0.002 0.001 HIS A 603 PHE 0.012 0.001 PHE A 115 TYR 0.016 0.001 TYR A 148 ARG 0.001 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 283) hydrogen bonds : angle 4.12073 ( 822) SS BOND : bond 0.00269 ( 1) SS BOND : angle 1.08148 ( 2) covalent geometry : bond 0.00325 ( 4400) covalent geometry : angle 0.51426 ( 6010) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.463 Fit side-chains REVERT: A 115 PHE cc_start: 0.8845 (t80) cc_final: 0.8600 (t80) REVERT: A 357 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7603 (t80) outliers start: 11 outliers final: 9 residues processed: 73 average time/residue: 0.1342 time to fit residues: 13.2195 Evaluate side-chains 75 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.133481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.112081 restraints weight = 5476.928| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.48 r_work: 0.3006 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4401 Z= 0.141 Angle : 0.510 5.749 6012 Z= 0.257 Chirality : 0.038 0.127 657 Planarity : 0.004 0.034 730 Dihedral : 4.345 54.302 579 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.91 % Allowed : 9.87 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.37), residues: 530 helix: 1.79 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.39 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 485 HIS 0.002 0.001 HIS A 603 PHE 0.019 0.001 PHE A 248 TYR 0.016 0.001 TYR A 80 ARG 0.001 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 283) hydrogen bonds : angle 4.08821 ( 822) SS BOND : bond 0.00271 ( 1) SS BOND : angle 1.07824 ( 2) covalent geometry : bond 0.00336 ( 4400) covalent geometry : angle 0.50985 ( 6010) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.423 Fit side-chains REVERT: A 115 PHE cc_start: 0.8870 (t80) cc_final: 0.8662 (t80) REVERT: A 150 MET cc_start: 0.8948 (tpp) cc_final: 0.8667 (tpt) REVERT: A 357 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7639 (t80) REVERT: A 504 MET cc_start: 0.8640 (mmm) cc_final: 0.8420 (mmm) REVERT: A 538 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7614 (m-40) outliers start: 13 outliers final: 9 residues processed: 73 average time/residue: 0.1271 time to fit residues: 12.5340 Evaluate side-chains 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.129971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.108038 restraints weight = 5478.942| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.50 r_work: 0.3001 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4401 Z= 0.145 Angle : 0.511 6.789 6012 Z= 0.257 Chirality : 0.039 0.127 657 Planarity : 0.004 0.034 730 Dihedral : 4.364 54.863 579 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.36 % Allowed : 10.99 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.38), residues: 530 helix: 1.83 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.29 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 555 HIS 0.002 0.001 HIS A 603 PHE 0.014 0.001 PHE A 248 TYR 0.016 0.001 TYR A 80 ARG 0.001 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 283) hydrogen bonds : angle 4.09510 ( 822) SS BOND : bond 0.00253 ( 1) SS BOND : angle 1.03987 ( 2) covalent geometry : bond 0.00345 ( 4400) covalent geometry : angle 0.51055 ( 6010) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.480 Fit side-chains REVERT: A 115 PHE cc_start: 0.8856 (t80) cc_final: 0.8623 (t80) REVERT: A 357 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7603 (t80) REVERT: A 504 MET cc_start: 0.8642 (mmm) cc_final: 0.8437 (mmm) REVERT: A 538 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7612 (m-40) outliers start: 15 outliers final: 10 residues processed: 78 average time/residue: 0.1531 time to fit residues: 15.8621 Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.0270 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.131787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109995 restraints weight = 5477.647| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.48 r_work: 0.3020 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4401 Z= 0.126 Angle : 0.505 6.143 6012 Z= 0.253 Chirality : 0.038 0.124 657 Planarity : 0.004 0.034 730 Dihedral : 4.321 55.473 579 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.36 % Allowed : 11.21 % Favored : 85.43 % 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: 1.83 (0.38), residues: 530 helix: 1.85 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.35 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 555 HIS 0.002 0.001 HIS A 603 PHE 0.014 0.001 PHE A 248 TYR 0.014 0.001 TYR A 80 ARG 0.001 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 283) hydrogen bonds : angle 4.05199 ( 822) SS BOND : bond 0.00261 ( 1) SS BOND : angle 1.04623 ( 2) covalent geometry : bond 0.00295 ( 4400) covalent geometry : angle 0.50472 ( 6010) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.426 Fit side-chains REVERT: A 115 PHE cc_start: 0.8798 (t80) cc_final: 0.8556 (t80) REVERT: A 357 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7589 (t80) REVERT: A 538 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7634 (m-40) outliers start: 15 outliers final: 11 residues processed: 77 average time/residue: 0.1305 time to fit residues: 13.3667 Evaluate side-chains 78 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.107761 restraints weight = 5406.824| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.55 r_work: 0.2999 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4401 Z= 0.142 Angle : 0.520 7.513 6012 Z= 0.259 Chirality : 0.038 0.126 657 Planarity : 0.004 0.034 730 Dihedral : 4.331 55.508 579 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.81 % Allowed : 11.21 % Favored : 84.98 % 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: 1.72 (0.38), residues: 530 helix: 1.72 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.35 (0.57), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 555 HIS 0.003 0.001 HIS A 575 PHE 0.012 0.001 PHE A 248 TYR 0.015 0.001 TYR A 80 ARG 0.001 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 283) hydrogen bonds : angle 4.07079 ( 822) SS BOND : bond 0.00251 ( 1) SS BOND : angle 1.03947 ( 2) covalent geometry : bond 0.00338 ( 4400) covalent geometry : angle 0.52018 ( 6010) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.423 Fit side-chains REVERT: A 115 PHE cc_start: 0.8794 (t80) cc_final: 0.8525 (t80) REVERT: A 150 MET cc_start: 0.9049 (mmm) cc_final: 0.8549 (tpt) REVERT: A 357 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7605 (t80) REVERT: A 538 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7622 (m-40) outliers start: 17 outliers final: 11 residues processed: 77 average time/residue: 0.1221 time to fit residues: 12.7342 Evaluate side-chains 78 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.0370 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.132943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.110492 restraints weight = 5479.072| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.55 r_work: 0.3029 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4401 Z= 0.122 Angle : 0.510 7.252 6012 Z= 0.256 Chirality : 0.038 0.124 657 Planarity : 0.004 0.034 730 Dihedral : 4.326 55.865 579 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.91 % Allowed : 12.11 % Favored : 84.98 % 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: 1.91 (0.38), residues: 530 helix: 1.91 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.32 (0.55), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 555 HIS 0.004 0.001 HIS A 575 PHE 0.014 0.001 PHE A 419 TYR 0.014 0.001 TYR A 80 ARG 0.001 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 283) hydrogen bonds : angle 4.02307 ( 822) SS BOND : bond 0.00226 ( 1) SS BOND : angle 1.02329 ( 2) covalent geometry : bond 0.00281 ( 4400) covalent geometry : angle 0.50996 ( 6010) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.477 Fit side-chains REVERT: A 115 PHE cc_start: 0.8824 (t80) cc_final: 0.8613 (t80) REVERT: A 150 MET cc_start: 0.9010 (mmm) cc_final: 0.8507 (tpt) REVERT: A 357 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7557 (t80) REVERT: A 538 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7618 (m-40) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.1478 time to fit residues: 14.9908 Evaluate side-chains 75 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 0.0570 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.107712 restraints weight = 5383.213| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.55 r_work: 0.3004 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4401 Z= 0.139 Angle : 0.524 7.177 6012 Z= 0.263 Chirality : 0.038 0.125 657 Planarity : 0.004 0.034 730 Dihedral : 4.333 55.737 579 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.69 % Allowed : 13.00 % Favored : 84.30 % 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: 1.87 (0.38), residues: 530 helix: 1.89 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.35 (0.55), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 555 HIS 0.003 0.001 HIS A 575 PHE 0.014 0.001 PHE A 419 TYR 0.015 0.001 TYR A 80 ARG 0.001 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 283) hydrogen bonds : angle 4.06310 ( 822) SS BOND : bond 0.00246 ( 1) SS BOND : angle 1.05940 ( 2) covalent geometry : bond 0.00331 ( 4400) covalent geometry : angle 0.52420 ( 6010) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.429 Fit side-chains REVERT: A 115 PHE cc_start: 0.8770 (t80) cc_final: 0.8515 (t80) REVERT: A 150 MET cc_start: 0.8990 (mmm) cc_final: 0.8506 (tpt) REVERT: A 357 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7564 (t80) REVERT: A 538 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7612 (m-40) outliers start: 12 outliers final: 10 residues processed: 73 average time/residue: 0.1383 time to fit residues: 13.5450 Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.131959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.109608 restraints weight = 5423.675| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.57 r_work: 0.3018 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4401 Z= 0.126 Angle : 0.511 7.162 6012 Z= 0.256 Chirality : 0.038 0.124 657 Planarity : 0.004 0.034 730 Dihedral : 4.306 56.010 579 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.69 % Allowed : 13.23 % Favored : 84.08 % 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: 1.93 (0.38), residues: 530 helix: 1.93 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.31 (0.55), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 555 HIS 0.003 0.001 HIS A 575 PHE 0.013 0.001 PHE A 419 TYR 0.014 0.001 TYR A 80 ARG 0.001 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 283) hydrogen bonds : angle 4.02529 ( 822) SS BOND : bond 0.00227 ( 1) SS BOND : angle 1.02916 ( 2) covalent geometry : bond 0.00295 ( 4400) covalent geometry : angle 0.51084 ( 6010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2391.41 seconds wall clock time: 41 minutes 54.27 seconds (2514.27 seconds total)