Starting phenix.real_space_refine on Wed Mar 5 16:16:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tz0_26201/03_2025/7tz0_26201.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tz0_26201/03_2025/7tz0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tz0_26201/03_2025/7tz0_26201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tz0_26201/03_2025/7tz0_26201.map" model { file = "/net/cci-nas-00/data/ceres_data/7tz0_26201/03_2025/7tz0_26201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tz0_26201/03_2025/7tz0_26201.cif" } resolution = 4.17 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= 0.100 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.20, per 1000 atoms: 0.82 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: 0.65 Conformation dependent library (CDL) restraints added in 341.1 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: 0.26 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: 0.61 Time building geometry restraints manager: 0.80 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: 0.130 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.040 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.810 ------------------------------------------------------------------------------- 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 2734 Z= 0.226 Angle : 0.624 9.374 3715 Z= 0.330 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 (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 (0.42), 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 TRP 0.003 0.001 TRP B 79 HIS 0.004 0.001 HIS B 52 PHE 0.032 0.001 PHE A 429 TYR 0.012 0.001 TYR A 495 ARG 0.004 0.000 ARG B 31 *********************** 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 : 0.288 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8385 (mp) cc_final: 0.7934 (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: 0.8260 (mt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1334 time to fit residues: 13.0651 Evaluate side-chains 72 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 30.0000 chunk 8 optimal weight: 0.1980 chunk 17 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- 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 = 0.4434 r_free = 0.4434 target = 0.189757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.160942 restraints weight = 6867.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.164829 restraints weight = 5011.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.168052 restraints weight = 3865.064| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2734 Z= 0.167 Angle : 0.573 6.468 3715 Z= 0.291 Chirality : 0.043 0.137 408 Planarity : 0.005 0.060 489 Dihedral : 4.598 18.322 376 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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: -1.65 (0.42), residues: 343 helix: -0.60 (0.45), residues: 113 sheet: -1.17 (0.90), residues: 30 loop : -1.38 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 353 HIS 0.006 0.002 HIS B 85 PHE 0.009 0.001 PHE A 490 TYR 0.011 0.001 TYR A 495 ARG 0.003 0.001 ARG A 355 *********************** 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 83 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7827 (mt0) cc_final: 0.7258 (mt0) REVERT: A 418 ILE cc_start: 0.8076 (mp) cc_final: 0.7534 (mp) REVERT: A 429 PHE cc_start: 0.7569 (t80) cc_final: 0.7208 (t80) REVERT: A 498 GLN cc_start: 0.8552 (mp10) cc_final: 0.8235 (mp10) REVERT: B 76 MET cc_start: 0.8354 (pmm) cc_final: 0.7965 (pmm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1138 time to fit residues: 11.7458 Evaluate side-chains 72 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4385 r_free = 0.4385 target = 0.185377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.156887 restraints weight = 7075.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.161167 restraints weight = 5043.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.164426 restraints weight = 3798.767| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2734 Z= 0.229 Angle : 0.670 10.433 3715 Z= 0.334 Chirality : 0.045 0.138 408 Planarity : 0.005 0.051 489 Dihedral : 5.333 20.287 376 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.42), residues: 343 helix: -0.71 (0.44), residues: 115 sheet: -1.65 (0.87), residues: 30 loop : -1.59 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 353 HIS 0.003 0.001 HIS B 52 PHE 0.016 0.002 PHE A 490 TYR 0.013 0.002 TYR A 380 ARG 0.006 0.001 ARG A 357 *********************** 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 85 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.300 Fit side-chains REVERT: A 374 PHE cc_start: 0.7607 (m-10) cc_final: 0.7309 (m-10) REVERT: A 418 ILE cc_start: 0.8256 (mp) cc_final: 0.7628 (mp) REVERT: A 429 PHE cc_start: 0.7628 (t80) cc_final: 0.7223 (t80) REVERT: A 498 GLN cc_start: 0.8288 (mp10) cc_final: 0.7894 (mp10) REVERT: B 76 MET cc_start: 0.8378 (pmm) cc_final: 0.7987 (pmm) REVERT: B 112 ASN cc_start: 0.7542 (t0) cc_final: 0.7127 (t0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1203 time to fit residues: 12.6238 Evaluate side-chains 72 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 10 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 2 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 = 0.187640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.160676 restraints weight = 7156.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.165009 restraints weight = 4991.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.168176 restraints weight = 3705.241| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2734 Z= 0.173 Angle : 0.623 9.890 3715 Z= 0.307 Chirality : 0.043 0.138 408 Planarity : 0.005 0.052 489 Dihedral : 5.028 18.881 376 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.35 % Allowed : 4.58 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.42), residues: 343 helix: -0.43 (0.45), residues: 115 sheet: -1.77 (0.87), residues: 30 loop : -1.59 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.006 0.001 HIS B 85 PHE 0.013 0.002 PHE B 150 TYR 0.013 0.001 TYR A 380 ARG 0.004 0.001 ARG A 357 *********************** 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 80 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.310 Fit side-chains REVERT: A 418 ILE cc_start: 0.8257 (mp) cc_final: 0.7549 (mp) REVERT: A 429 PHE cc_start: 0.7570 (t80) cc_final: 0.7228 (t80) REVERT: A 498 GLN cc_start: 0.8245 (mp10) cc_final: 0.7842 (mp10) REVERT: B 76 MET cc_start: 0.8364 (pmm) cc_final: 0.7997 (pmm) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.1214 time to fit residues: 12.0904 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 : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 0.3980 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 21 optimal weight: 0.1980 chunk 23 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 = 0.189848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.162750 restraints weight = 6853.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.167169 restraints weight = 4693.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.170490 restraints weight = 3425.178| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2734 Z= 0.159 Angle : 0.615 9.720 3715 Z= 0.299 Chirality : 0.043 0.133 408 Planarity : 0.005 0.050 489 Dihedral : 4.864 19.327 376 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % 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 (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: -1.64 (0.42), residues: 343 helix: -0.29 (0.46), residues: 115 sheet: -2.49 (0.88), residues: 25 loop : -1.39 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.004 0.001 HIS B 85 PHE 0.010 0.001 PHE A 490 TYR 0.015 0.001 TYR A 380 ARG 0.003 0.000 ARG A 357 *********************** 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 84 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8292 (mp) cc_final: 0.7574 (mp) REVERT: A 429 PHE cc_start: 0.7541 (t80) cc_final: 0.7189 (t80) REVERT: A 498 GLN cc_start: 0.8330 (mp10) cc_final: 0.7944 (mp10) REVERT: B 76 MET cc_start: 0.8334 (pmm) cc_final: 0.7963 (pmm) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.1121 time to fit residues: 11.6040 Evaluate side-chains 69 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 36 ASN B 135 ASN B 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.193037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.165418 restraints weight = 6857.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.169836 restraints weight = 4778.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.173143 restraints weight = 3526.469| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2734 Z= 0.135 Angle : 0.600 9.260 3715 Z= 0.291 Chirality : 0.043 0.132 408 Planarity : 0.005 0.048 489 Dihedral : 4.449 18.290 376 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.70 % Allowed : 1.06 % 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 (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: -1.50 (0.43), residues: 343 helix: -0.10 (0.47), residues: 120 sheet: -1.69 (0.85), residues: 31 loop : -1.47 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS B 52 PHE 0.005 0.001 PHE A 400 TYR 0.010 0.001 TYR A 495 ARG 0.002 0.000 ARG A 346 *********************** 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 88 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7639 (t0) cc_final: 0.6459 (t0) REVERT: A 418 ILE cc_start: 0.8277 (mp) cc_final: 0.7581 (mp) REVERT: A 429 PHE cc_start: 0.7550 (t80) cc_final: 0.7196 (t80) REVERT: A 498 GLN cc_start: 0.8327 (mp10) cc_final: 0.7967 (mp10) REVERT: B 76 MET cc_start: 0.8315 (pmm) cc_final: 0.7931 (pmm) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.1213 time to fit residues: 13.0636 Evaluate side-chains 67 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 40.0000 chunk 23 optimal weight: 10.0000 overall best weight: 5.5186 ------------------------------------------------------------------------------- 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 112 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.186833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.159934 restraints weight = 7357.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.164206 restraints weight = 4965.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.167520 restraints weight = 3599.238| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2734 Z= 0.235 Angle : 0.680 11.948 3715 Z= 0.340 Chirality : 0.044 0.141 408 Planarity : 0.005 0.049 489 Dihedral : 5.224 18.988 376 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % 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 (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: -1.69 (0.43), residues: 343 helix: -0.24 (0.46), residues: 114 sheet: -1.86 (0.82), residues: 31 loop : -1.55 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 353 HIS 0.004 0.001 HIS B 85 PHE 0.017 0.002 PHE A 490 TYR 0.010 0.002 TYR A 495 ARG 0.006 0.001 ARG A 357 *********************** 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 83 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.268 Fit side-chains REVERT: A 418 ILE cc_start: 0.8301 (mp) cc_final: 0.7627 (mp) REVERT: A 429 PHE cc_start: 0.7649 (t80) cc_final: 0.7308 (t80) REVERT: A 498 GLN cc_start: 0.8231 (mp10) cc_final: 0.7847 (mp10) REVERT: B 76 MET cc_start: 0.8285 (pmm) cc_final: 0.7828 (pmm) outliers start: 2 outliers final: 0 residues processed: 82 average time/residue: 0.1138 time to fit residues: 11.6201 Evaluate side-chains 70 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 0.0370 chunk 23 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.2066 ------------------------------------------------------------------------------- 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 112 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 = 0.4395 r_free = 0.4395 target = 0.188417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.161904 restraints weight = 6884.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.166038 restraints weight = 4748.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.169149 restraints weight = 3485.274| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2734 Z= 0.192 Angle : 0.650 11.596 3715 Z= 0.319 Chirality : 0.044 0.139 408 Planarity : 0.005 0.048 489 Dihedral : 5.139 18.843 376 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % 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 (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: -1.76 (0.44), residues: 343 helix: -0.16 (0.48), residues: 113 sheet: -2.01 (0.81), residues: 33 loop : -1.65 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 353 HIS 0.004 0.001 HIS B 85 PHE 0.029 0.002 PHE A 347 TYR 0.011 0.001 TYR A 495 ARG 0.004 0.001 ARG A 357 *********************** 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 82 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.271 Fit side-chains REVERT: A 418 ILE cc_start: 0.8307 (mp) cc_final: 0.7531 (mp) REVERT: A 429 PHE cc_start: 0.7687 (t80) cc_final: 0.7381 (t80) REVERT: A 498 GLN cc_start: 0.8179 (mp10) cc_final: 0.7834 (mp10) REVERT: B 76 MET cc_start: 0.8215 (pmm) cc_final: 0.7783 (pmm) outliers start: 2 outliers final: 1 residues processed: 81 average time/residue: 0.1222 time to fit residues: 12.2995 Evaluate side-chains 72 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 40.0000 chunk 30 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.187519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.161609 restraints weight = 7153.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.165595 restraints weight = 4947.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.168678 restraints weight = 3653.994| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2734 Z= 0.182 Angle : 0.658 11.511 3715 Z= 0.323 Chirality : 0.043 0.139 408 Planarity : 0.005 0.048 489 Dihedral : 5.026 19.136 376 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.35 % Allowed : 1.06 % Favored : 98.59 % 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: -1.76 (0.44), residues: 343 helix: -0.16 (0.47), residues: 112 sheet: -2.63 (0.87), residues: 27 loop : -1.57 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 353 HIS 0.003 0.001 HIS B 85 PHE 0.021 0.001 PHE A 347 TYR 0.018 0.001 TYR A 396 ARG 0.004 0.000 ARG A 357 *********************** 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 78 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.299 Fit side-chains REVERT: A 418 ILE cc_start: 0.8322 (mp) cc_final: 0.7584 (mp) REVERT: A 429 PHE cc_start: 0.7620 (t80) cc_final: 0.7312 (t80) REVERT: A 498 GLN cc_start: 0.8155 (mp10) cc_final: 0.7802 (mp10) REVERT: A 506 GLN cc_start: 0.5321 (tm-30) cc_final: 0.5078 (tm-30) REVERT: B 76 MET cc_start: 0.8204 (pmm) cc_final: 0.7779 (pmm) outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1176 time to fit residues: 11.2052 Evaluate side-chains 69 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 0.0870 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- 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 ** 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 = 0.4374 r_free = 0.4374 target = 0.185440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.159659 restraints weight = 7260.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.163786 restraints weight = 4971.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.166855 restraints weight = 3665.055| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2734 Z= 0.216 Angle : 0.698 13.415 3715 Z= 0.341 Chirality : 0.045 0.166 408 Planarity : 0.005 0.047 489 Dihedral : 5.270 19.267 376 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % 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 (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: -2.01 (0.43), residues: 343 helix: -0.40 (0.46), residues: 112 sheet: -2.24 (0.79), residues: 33 loop : -1.77 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 353 HIS 0.003 0.001 HIS B 85 PHE 0.015 0.002 PHE A 490 TYR 0.013 0.002 TYR A 453 ARG 0.005 0.001 ARG A 357 ********************** 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: 0 poor density : 81 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8359 (mp) cc_final: 0.7688 (mp) REVERT: A 429 PHE cc_start: 0.7861 (t80) cc_final: 0.7486 (t80) REVERT: A 498 GLN cc_start: 0.8084 (mp10) cc_final: 0.7763 (mp10) REVERT: A 506 GLN cc_start: 0.5422 (tm-30) cc_final: 0.5201 (tm-30) REVERT: B 76 MET cc_start: 0.8145 (pmm) cc_final: 0.7739 (pmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1251 time to fit residues: 12.1766 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 : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.186822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.160187 restraints weight = 6937.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.164557 restraints weight = 4714.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.167839 restraints weight = 3422.821| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2734 Z= 0.235 Angle : 0.685 14.052 3715 Z= 0.342 Chirality : 0.045 0.157 408 Planarity : 0.005 0.046 489 Dihedral : 5.482 19.459 376 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % 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 (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: -2.15 (0.42), residues: 343 helix: -0.59 (0.44), residues: 111 sheet: -2.76 (0.84), residues: 26 loop : -1.77 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 353 HIS 0.004 0.001 HIS B 85 PHE 0.018 0.002 PHE A 347 TYR 0.014 0.002 TYR A 495 ARG 0.006 0.001 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1274.73 seconds wall clock time: 22 minutes 43.20 seconds (1363.20 seconds total)