Starting phenix.real_space_refine on Tue Mar 3 11:05:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tz0_26201/03_2026/7tz0_26201.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tz0_26201/03_2026/7tz0_26201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tz0_26201/03_2026/7tz0_26201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tz0_26201/03_2026/7tz0_26201.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tz0_26201/03_2026/7tz0_26201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tz0_26201/03_2026/7tz0_26201.map" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.100 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 12 5.16 5 C 1699 2.51 5 N 453 2.21 5 O 510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2674 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1521 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 10, 'TRANS': 181} Chain: "B" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Time building chain proxies: 0.85, per 1000 atoms: 0.32 Number of scatterers: 2674 At special positions: 0 Unit cell: (58.491, 66.348, 96.903, 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 12 16.00 O 510 8.00 N 453 7.00 C 1699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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: 0.21 Conformation dependent library (CDL) restraints added in 82.4 milliseconds 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 632 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 36.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.304A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'B' and resid 16 through 25 removed outlier: 3.542A pdb=" N GLU B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.522A pdb=" N LEU B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 4.064A pdb=" N TYR B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 93 through 103 removed outlier: 4.008A pdb=" N GLU B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.528A pdb=" N ARG B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.617A pdb=" N VAL B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 135 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 removed outlier: 3.599A pdb=" N ASP B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.839A pdb=" N ALA B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 164 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 397 through 402 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 72 hydrogen bonds defined for protein. 207 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: 0.33 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 889 1.35 - 1.46: 646 1.46 - 1.58: 1184 1.58 - 1.70: 1 1.70 - 1.81: 14 Bond restraints: 2734 Sorted by residual: bond pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 1.492 1.605 -0.113 5.00e-02 4.00e+02 5.13e+00 bond pdb=" CB PRO B 50 " pdb=" CG PRO B 50 " ideal model delta sigma weight residual 1.492 1.553 -0.061 5.00e-02 4.00e+02 1.47e+00 bond pdb=" CB LYS A 458 " pdb=" CG LYS A 458 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.11e-01 bond pdb=" CG PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.503 1.533 -0.030 3.40e-02 8.65e+02 8.03e-01 bond pdb=" CB ARG B 31 " pdb=" CG ARG B 31 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.69e-01 ... (remaining 2729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 3639 1.87 - 3.75: 64 3.75 - 5.62: 9 5.62 - 7.50: 2 7.50 - 9.37: 1 Bond angle restraints: 3715 Sorted by residual: angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 104.86 7.14 1.40e+00 5.10e-01 2.60e+01 angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 113.42 108.54 4.88 1.17e+00 7.31e-01 1.74e+01 angle pdb=" CA PRO B 50 " pdb=" N PRO B 50 " pdb=" CD PRO B 50 " ideal model delta sigma weight residual 112.00 107.42 4.58 1.40e+00 5.10e-01 1.07e+01 angle pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " ideal model delta sigma weight residual 116.30 125.67 -9.37 3.50e+00 8.16e-02 7.17e+00 angle pdb=" CA LYS A 458 " pdb=" CB LYS A 458 " pdb=" CG LYS A 458 " ideal model delta sigma weight residual 114.10 119.44 -5.34 2.00e+00 2.50e-01 7.14e+00 ... (remaining 3710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 1429 14.80 - 29.59: 143 29.59 - 44.39: 32 44.39 - 59.18: 8 59.18 - 73.98: 2 Dihedral angle restraints: 1614 sinusoidal: 619 harmonic: 995 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 19.02 73.98 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -144.38 58.38 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 46.65 46.35 1 1.00e+01 1.00e-02 2.97e+01 ... (remaining 1611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 223 0.028 - 0.056: 115 0.056 - 0.084: 45 0.084 - 0.112: 19 0.112 - 0.140: 6 Chirality restraints: 408 Sorted by residual: chirality pdb=" CA PRO B 50 " pdb=" N PRO B 50 " pdb=" C PRO B 50 " pdb=" CB PRO B 50 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA PRO A 491 " pdb=" N PRO A 491 " pdb=" C PRO A 491 " pdb=" CB PRO A 491 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA VAL A 382 " pdb=" N VAL A 382 " pdb=" C VAL A 382 " pdb=" CB VAL A 382 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 405 not shown) Planarity restraints: 489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " -0.075 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A 384 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 49 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO B 50 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 50 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 50 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 360 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C ASN A 360 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN A 360 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS A 361 " -0.012 2.00e-02 2.50e+03 ... (remaining 486 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 715 2.79 - 3.32: 2669 3.32 - 3.85: 4201 3.85 - 4.37: 4974 4.37 - 4.90: 7820 Nonbonded interactions: 20379 Sorted by model distance: nonbonded pdb=" OG1 THR A 415 " pdb=" OD2 ASP A 420 " model vdw 2.265 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.271 3.040 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 2.277 3.120 nonbonded pdb=" NH1 ARG A 357 " pdb=" O ILE A 358 " model vdw 2.281 3.120 nonbonded pdb=" OG1 THR B 82 " pdb=" ND1 HIS B 85 " model vdw 2.306 3.120 ... (remaining 20374 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 group one per residue 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: 0.080 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.800 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 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 : 0.003 0.113 2738 Z= 0.114 Angle : 0.626 9.374 3723 Z= 0.331 Chirality : 0.041 0.140 408 Planarity : 0.007 0.110 489 Dihedral : 12.380 69.766 970 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.42), residues: 343 helix: -0.69 (0.47), residues: 106 sheet: -1.48 (1.07), residues: 24 loop : -1.37 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.012 0.001 TYR A 495 PHE 0.032 0.001 PHE A 429 TRP 0.003 0.001 TRP B 79 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2734) covalent geometry : angle 0.62432 ( 3715) SS BOND : bond 0.00223 ( 4) SS BOND : angle 1.28132 ( 8) hydrogen bonds : bond 0.26316 ( 72) hydrogen bonds : angle 7.56412 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8385 (mp) cc_final: 0.7927 (mp) REVERT: A 498 GLN cc_start: 0.8587 (mp10) cc_final: 0.8268 (mp10) REVERT: B 66 LEU cc_start: 0.8491 (mt) cc_final: 0.8261 (mt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0536 time to fit residues: 5.3139 Evaluate side-chains 71 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 30.0000 chunk 2 optimal weight: 40.0000 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.0670 chunk 31 optimal weight: 40.0000 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.191194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.161981 restraints weight = 6901.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.165879 restraints weight = 5020.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.169084 restraints weight = 3860.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.171434 restraints weight = 3081.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.173443 restraints weight = 2546.028| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 2738 Z= 0.101 Angle : 0.563 6.425 3723 Z= 0.284 Chirality : 0.042 0.136 408 Planarity : 0.005 0.060 489 Dihedral : 4.479 18.303 376 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.42), residues: 343 helix: -0.53 (0.46), residues: 113 sheet: -1.23 (0.89), residues: 30 loop : -1.35 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.012 0.001 TYR A 495 PHE 0.008 0.001 PHE B 150 TRP 0.003 0.001 TRP A 353 HIS 0.006 0.002 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 2734) covalent geometry : angle 0.55990 ( 3715) SS BOND : bond 0.00308 ( 4) SS BOND : angle 1.35944 ( 8) hydrogen bonds : bond 0.02673 ( 72) hydrogen bonds : angle 5.40111 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8007 (mp) cc_final: 0.7436 (mp) REVERT: A 429 PHE cc_start: 0.7607 (t80) cc_final: 0.7297 (t80) REVERT: A 498 GLN cc_start: 0.8547 (mp10) cc_final: 0.8220 (mp10) REVERT: B 76 MET cc_start: 0.8327 (pmm) cc_final: 0.7931 (pmm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0446 time to fit residues: 4.7996 Evaluate side-chains 74 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 17 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 422 ASN B 36 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.185611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.156484 restraints weight = 7240.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.160580 restraints weight = 5207.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.163650 restraints weight = 3983.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.166169 restraints weight = 3174.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.168012 restraints weight = 2592.628| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 2738 Z= 0.152 Angle : 0.633 8.857 3723 Z= 0.319 Chirality : 0.044 0.135 408 Planarity : 0.005 0.053 489 Dihedral : 5.055 20.578 376 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.35 % Allowed : 3.87 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.41), residues: 343 helix: -0.62 (0.45), residues: 115 sheet: -1.62 (0.85), residues: 30 loop : -1.58 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.011 0.002 TYR A 380 PHE 0.014 0.002 PHE B 150 TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2734) covalent geometry : angle 0.62695 ( 3715) SS BOND : bond 0.00929 ( 4) SS BOND : angle 2.00450 ( 8) hydrogen bonds : bond 0.03075 ( 72) hydrogen bonds : angle 5.34193 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.099 Fit side-chains REVERT: A 340 GLU cc_start: 0.7526 (pt0) cc_final: 0.7313 (tt0) REVERT: A 374 PHE cc_start: 0.7484 (m-10) cc_final: 0.7239 (m-10) REVERT: A 418 ILE cc_start: 0.8208 (mp) cc_final: 0.7606 (mp) REVERT: A 429 PHE cc_start: 0.7616 (t80) cc_final: 0.7247 (t80) REVERT: A 498 GLN cc_start: 0.8418 (mp10) cc_final: 0.8060 (mp10) REVERT: B 76 MET cc_start: 0.8405 (pmm) cc_final: 0.8036 (pmm) REVERT: B 112 ASN cc_start: 0.7412 (t0) cc_final: 0.7051 (t0) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.0503 time to fit residues: 5.1393 Evaluate side-chains 71 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 0.0270 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.189202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.161440 restraints weight = 7370.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.165840 restraints weight = 5174.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.169155 restraints weight = 3854.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.171470 restraints weight = 2998.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.173276 restraints weight = 2438.985| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2738 Z= 0.117 Angle : 0.614 8.953 3723 Z= 0.302 Chirality : 0.043 0.134 408 Planarity : 0.005 0.052 489 Dihedral : 4.896 19.367 376 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.42), residues: 343 helix: -0.60 (0.44), residues: 121 sheet: -1.48 (0.86), residues: 31 loop : -1.49 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.010 0.001 TYR A 495 PHE 0.010 0.001 PHE B 150 TRP 0.006 0.001 TRP A 353 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2734) covalent geometry : angle 0.60755 ( 3715) SS BOND : bond 0.00149 ( 4) SS BOND : angle 2.05658 ( 8) hydrogen bonds : bond 0.02651 ( 72) hydrogen bonds : angle 5.18857 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.070 Fit side-chains REVERT: A 374 PHE cc_start: 0.7529 (m-10) cc_final: 0.7197 (m-10) REVERT: A 418 ILE cc_start: 0.8198 (mp) cc_final: 0.7502 (mp) REVERT: A 429 PHE cc_start: 0.7509 (t80) cc_final: 0.7172 (t80) REVERT: A 498 GLN cc_start: 0.8298 (mp10) cc_final: 0.7897 (mp10) REVERT: B 76 MET cc_start: 0.8354 (pmm) cc_final: 0.7981 (pmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0438 time to fit residues: 4.2900 Evaluate side-chains 62 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 388 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.184325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.156664 restraints weight = 7072.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.160980 restraints weight = 4886.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.164113 restraints weight = 3609.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.166405 restraints weight = 2796.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.168172 restraints weight = 2258.196| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2738 Z= 0.168 Angle : 0.693 12.483 3723 Z= 0.344 Chirality : 0.044 0.139 408 Planarity : 0.005 0.049 489 Dihedral : 5.478 19.589 376 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.35 % Allowed : 2.46 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.42), residues: 343 helix: -0.63 (0.44), residues: 115 sheet: -1.71 (0.86), residues: 31 loop : -1.67 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.010 0.002 TYR A 396 PHE 0.018 0.002 PHE A 490 TRP 0.007 0.002 TRP A 353 HIS 0.005 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 2734) covalent geometry : angle 0.68176 ( 3715) SS BOND : bond 0.00488 ( 4) SS BOND : angle 2.71204 ( 8) hydrogen bonds : bond 0.03128 ( 72) hydrogen bonds : angle 5.36210 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.093 Fit side-chains REVERT: A 418 ILE cc_start: 0.8284 (mp) cc_final: 0.7584 (mp) REVERT: A 429 PHE cc_start: 0.7659 (t80) cc_final: 0.7331 (t80) REVERT: A 498 GLN cc_start: 0.8078 (mp10) cc_final: 0.7651 (mp10) REVERT: B 76 MET cc_start: 0.8354 (pmm) cc_final: 0.7911 (pmm) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.0418 time to fit residues: 4.2539 Evaluate side-chains 66 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 15 optimal weight: 7.9990 chunk 31 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 112 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.185897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.159052 restraints weight = 6988.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.163300 restraints weight = 4813.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.166485 restraints weight = 3519.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.168771 restraints weight = 2708.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.170551 restraints weight = 2171.418| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2738 Z= 0.140 Angle : 0.682 12.540 3723 Z= 0.331 Chirality : 0.044 0.139 408 Planarity : 0.005 0.046 489 Dihedral : 5.213 18.735 376 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.70 % Allowed : 2.11 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.42), residues: 343 helix: -0.45 (0.45), residues: 115 sheet: -2.10 (0.85), residues: 30 loop : -1.69 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 357 TYR 0.017 0.001 TYR A 396 PHE 0.014 0.002 PHE B 150 TRP 0.010 0.002 TRP A 353 HIS 0.004 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2734) covalent geometry : angle 0.67363 ( 3715) SS BOND : bond 0.00369 ( 4) SS BOND : angle 2.33492 ( 8) hydrogen bonds : bond 0.02869 ( 72) hydrogen bonds : angle 5.23898 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8324 (mp) cc_final: 0.7595 (mp) REVERT: A 429 PHE cc_start: 0.7667 (t80) cc_final: 0.7324 (t80) REVERT: A 498 GLN cc_start: 0.8023 (mp10) cc_final: 0.7596 (mp10) REVERT: B 76 MET cc_start: 0.8250 (pmm) cc_final: 0.7836 (pmm) outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 0.0429 time to fit residues: 4.4049 Evaluate side-chains 64 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 0.0050 chunk 19 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 0.0040 chunk 14 optimal weight: 0.0980 chunk 18 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 overall best weight: 2.4210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.189647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.162156 restraints weight = 7004.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.166359 restraints weight = 4917.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.169495 restraints weight = 3658.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.171989 restraints weight = 2856.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.173686 restraints weight = 2298.203| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2738 Z= 0.106 Angle : 0.643 10.357 3723 Z= 0.311 Chirality : 0.043 0.137 408 Planarity : 0.005 0.048 489 Dihedral : 4.937 19.387 376 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.35 % Allowed : 1.41 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.43), residues: 343 helix: -0.30 (0.46), residues: 121 sheet: -2.11 (0.82), residues: 30 loop : -1.52 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.011 0.001 TYR A 495 PHE 0.019 0.001 PHE A 347 TRP 0.006 0.001 TRP B 79 HIS 0.004 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 2734) covalent geometry : angle 0.63842 ( 3715) SS BOND : bond 0.00117 ( 4) SS BOND : angle 1.70768 ( 8) hydrogen bonds : bond 0.02733 ( 72) hydrogen bonds : angle 5.10894 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.075 Fit side-chains REVERT: A 418 ILE cc_start: 0.8278 (mp) cc_final: 0.7563 (mp) REVERT: A 429 PHE cc_start: 0.7508 (t80) cc_final: 0.7172 (t80) REVERT: A 498 GLN cc_start: 0.8102 (mp10) cc_final: 0.7714 (mp10) REVERT: B 76 MET cc_start: 0.8222 (pmm) cc_final: 0.7811 (pmm) outliers start: 1 outliers final: 1 residues processed: 82 average time/residue: 0.0501 time to fit residues: 5.0877 Evaluate side-chains 73 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.0040 chunk 14 optimal weight: 0.0370 chunk 31 optimal weight: 40.0000 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 135 ASN B 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.191935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.165156 restraints weight = 7246.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.169244 restraints weight = 5189.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.172362 restraints weight = 3909.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.174569 restraints weight = 3060.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.176399 restraints weight = 2505.306| |-----------------------------------------------------------------------------| r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2738 Z= 0.098 Angle : 0.603 9.730 3723 Z= 0.296 Chirality : 0.043 0.136 408 Planarity : 0.005 0.050 489 Dihedral : 4.640 18.170 376 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.70 % Allowed : 1.41 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.43), residues: 343 helix: -0.06 (0.47), residues: 120 sheet: -1.83 (0.82), residues: 31 loop : -1.49 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.014 0.001 TYR A 495 PHE 0.018 0.001 PHE A 347 TRP 0.011 0.002 TRP A 353 HIS 0.003 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 2734) covalent geometry : angle 0.59966 ( 3715) SS BOND : bond 0.00168 ( 4) SS BOND : angle 1.45456 ( 8) hydrogen bonds : bond 0.02323 ( 72) hydrogen bonds : angle 4.82693 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.163 Fit side-chains REVERT: A 418 ILE cc_start: 0.8256 (mp) cc_final: 0.7523 (mp) REVERT: A 429 PHE cc_start: 0.7401 (t80) cc_final: 0.7118 (t80) REVERT: A 498 GLN cc_start: 0.8179 (mp10) cc_final: 0.7812 (mp10) REVERT: B 76 MET cc_start: 0.8159 (pmm) cc_final: 0.7791 (pmm) outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 0.0511 time to fit residues: 5.1431 Evaluate side-chains 71 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 2 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 30.0000 chunk 3 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 422 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.188655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.162782 restraints weight = 7368.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.166797 restraints weight = 5209.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.169969 restraints weight = 3862.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.172173 restraints weight = 2986.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.174008 restraints weight = 2411.639| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2738 Z= 0.120 Angle : 0.638 9.830 3723 Z= 0.315 Chirality : 0.043 0.136 408 Planarity : 0.005 0.050 489 Dihedral : 4.780 18.975 376 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.70 % Allowed : 0.35 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.44), residues: 343 helix: -0.11 (0.47), residues: 120 sheet: -2.05 (0.81), residues: 31 loop : -1.46 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 357 TYR 0.011 0.001 TYR A 495 PHE 0.017 0.002 PHE A 347 TRP 0.010 0.002 TRP A 353 HIS 0.004 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2734) covalent geometry : angle 0.63304 ( 3715) SS BOND : bond 0.00234 ( 4) SS BOND : angle 1.87295 ( 8) hydrogen bonds : bond 0.02648 ( 72) hydrogen bonds : angle 4.91247 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.057 Fit side-chains REVERT: A 418 ILE cc_start: 0.8267 (mp) cc_final: 0.7587 (mp) REVERT: A 429 PHE cc_start: 0.7557 (t80) cc_final: 0.7263 (t80) REVERT: A 498 GLN cc_start: 0.8145 (mp10) cc_final: 0.7768 (mp10) REVERT: A 506 GLN cc_start: 0.5236 (tm-30) cc_final: 0.4941 (tm-30) REVERT: B 76 MET cc_start: 0.8137 (pmm) cc_final: 0.7745 (pmm) outliers start: 2 outliers final: 0 residues processed: 79 average time/residue: 0.0513 time to fit residues: 4.9719 Evaluate side-chains 68 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.0870 chunk 31 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 112 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.188537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.163367 restraints weight = 7343.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.167414 restraints weight = 5108.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.170620 restraints weight = 3781.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.173006 restraints weight = 2908.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.174636 restraints weight = 2321.717| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2738 Z= 0.126 Angle : 0.650 10.896 3723 Z= 0.321 Chirality : 0.043 0.140 408 Planarity : 0.005 0.049 489 Dihedral : 4.911 18.809 376 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.35 % Allowed : 0.70 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.43), residues: 343 helix: -0.25 (0.46), residues: 118 sheet: -2.31 (0.77), residues: 33 loop : -1.56 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 355 TYR 0.010 0.001 TYR A 495 PHE 0.018 0.002 PHE A 347 TRP 0.012 0.002 TRP A 353 HIS 0.004 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 2734) covalent geometry : angle 0.64427 ( 3715) SS BOND : bond 0.00210 ( 4) SS BOND : angle 2.00393 ( 8) hydrogen bonds : bond 0.02775 ( 72) hydrogen bonds : angle 4.95207 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8277 (mp) cc_final: 0.7557 (mp) REVERT: A 429 PHE cc_start: 0.7571 (t80) cc_final: 0.7276 (t80) REVERT: A 498 GLN cc_start: 0.8073 (mp10) cc_final: 0.7714 (mp10) REVERT: A 506 GLN cc_start: 0.5240 (tm-30) cc_final: 0.4953 (tm-30) REVERT: B 76 MET cc_start: 0.8037 (pmm) cc_final: 0.7669 (pmm) outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.0504 time to fit residues: 4.9555 Evaluate side-chains 71 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 40.0000 chunk 7 optimal weight: 8.9990 chunk 26 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 422 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.187627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.162414 restraints weight = 7297.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.166586 restraints weight = 5029.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.169712 restraints weight = 3691.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.171980 restraints weight = 2845.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.173630 restraints weight = 2273.580| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2738 Z= 0.138 Angle : 0.673 12.040 3723 Z= 0.332 Chirality : 0.044 0.144 408 Planarity : 0.005 0.049 489 Dihedral : 5.105 19.546 376 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.35 % Allowed : 0.35 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.43), residues: 343 helix: -0.27 (0.46), residues: 112 sheet: -2.15 (0.79), residues: 32 loop : -1.68 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 355 TYR 0.013 0.001 TYR A 495 PHE 0.016 0.002 PHE A 347 TRP 0.013 0.002 TRP A 353 HIS 0.005 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 2734) covalent geometry : angle 0.66621 ( 3715) SS BOND : bond 0.00300 ( 4) SS BOND : angle 2.15341 ( 8) hydrogen bonds : bond 0.02741 ( 72) hydrogen bonds : angle 5.04998 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 664.14 seconds wall clock time: 12 minutes 0.85 seconds (720.85 seconds total)