Starting phenix.real_space_refine on Wed Mar 5 22:21:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xop_33355/03_2025/7xop_33355.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xop_33355/03_2025/7xop_33355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xop_33355/03_2025/7xop_33355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xop_33355/03_2025/7xop_33355.map" model { file = "/net/cci-nas-00/data/ceres_data/7xop_33355/03_2025/7xop_33355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xop_33355/03_2025/7xop_33355.cif" } resolution = 3.2 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= 0.006 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 20 5.16 5 C 2397 2.51 5 N 665 2.21 5 O 773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 2.95, per 1000 atoms: 0.77 Number of scatterers: 3855 At special positions: 0 Unit cell: (72.21, 85.26, 71.34, 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 20 16.00 O 773 8.00 N 665 7.00 C 2397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 448.5 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 7 sheets defined 58.6% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'K' and resid 9 through 29 removed outlier: 4.177A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.773A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 Processing helix chain 'K' and resid 88 through 110 removed outlier: 3.575A pdb=" N GLY K 110 " --> pdb=" O ALA K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 removed outlier: 3.558A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 256 through 269 Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 338 through 355 Processing helix chain 'K' and resid 359 through 375 removed outlier: 4.053A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 427 removed outlier: 3.834A pdb=" N ILE K 420 " --> pdb=" O GLY K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 458 Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 461 through 472 Processing helix chain 'K' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'K' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'K' and resid 174 through 179 removed outlier: 6.530A pdb=" N VAL K 174 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE K 379 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR K 176 " --> pdb=" O ILE K 379 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL K 381 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLU K 178 " --> pdb=" O VAL K 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 192 through 193 Processing sheet with id=AA5, first strand: chain 'K' and resid 273 through 277 Processing sheet with id=AA6, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'K' and resid 476 through 479 removed outlier: 3.670A pdb=" N GLU K 484 " --> pdb=" O ASN K 479 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1340 1.34 - 1.46: 490 1.46 - 1.57: 2016 1.57 - 1.69: 0 1.69 - 1.80: 37 Bond restraints: 3883 Sorted by residual: bond pdb=" SD MET K 520 " pdb=" CE MET K 520 " ideal model delta sigma weight residual 1.791 1.759 0.032 2.50e-02 1.60e+03 1.62e+00 bond pdb=" CA MET K 520 " pdb=" CB MET K 520 " ideal model delta sigma weight residual 1.536 1.510 0.026 2.08e-02 2.31e+03 1.54e+00 bond pdb=" CB MET K 520 " pdb=" CG MET K 520 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" CA GLY K 256 " pdb=" C GLY K 256 " ideal model delta sigma weight residual 1.520 1.508 0.012 1.28e-02 6.10e+03 8.15e-01 bond pdb=" SD MET K 16 " pdb=" CE MET K 16 " ideal model delta sigma weight residual 1.791 1.771 0.020 2.50e-02 1.60e+03 6.30e-01 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 5166 1.55 - 3.10: 68 3.10 - 4.65: 4 4.65 - 6.20: 4 6.20 - 7.75: 1 Bond angle restraints: 5243 Sorted by residual: angle pdb=" CB MET K 520 " pdb=" CG MET K 520 " pdb=" SD MET K 520 " ideal model delta sigma weight residual 112.70 104.95 7.75 3.00e+00 1.11e-01 6.67e+00 angle pdb=" N ALA K 449 " pdb=" CA ALA K 449 " pdb=" C ALA K 449 " ideal model delta sigma weight residual 112.75 115.50 -2.75 1.36e+00 5.41e-01 4.09e+00 angle pdb=" CB MET K 166 " pdb=" CG MET K 166 " pdb=" SD MET K 166 " ideal model delta sigma weight residual 112.70 118.43 -5.73 3.00e+00 1.11e-01 3.64e+00 angle pdb=" C GLU K 409 " pdb=" N GLY K 410 " pdb=" CA GLY K 410 " ideal model delta sigma weight residual 121.45 118.95 2.50 1.54e+00 4.22e-01 2.63e+00 angle pdb=" C ASP K 490 " pdb=" N MET K 491 " pdb=" CA MET K 491 " ideal model delta sigma weight residual 122.65 120.08 2.57 1.60e+00 3.91e-01 2.58e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 2262 17.68 - 35.37: 126 35.37 - 53.05: 20 53.05 - 70.73: 3 70.73 - 88.41: 1 Dihedral angle restraints: 2412 sinusoidal: 934 harmonic: 1478 Sorted by residual: dihedral pdb=" CA ASP K 224 " pdb=" CB ASP K 224 " pdb=" CG ASP K 224 " pdb=" OD1 ASP K 224 " ideal model delta sinusoidal sigma weight residual -30.00 -86.40 56.40 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU K 102 " pdb=" CG GLU K 102 " pdb=" CD GLU K 102 " pdb=" OE1 GLU K 102 " ideal model delta sinusoidal sigma weight residual 0.00 88.41 -88.41 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA MET K 491 " pdb=" C MET K 491 " pdb=" N GLY K 492 " pdb=" CA GLY K 492 " ideal model delta harmonic sigma weight residual 180.00 164.92 15.08 0 5.00e+00 4.00e-02 9.09e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 360 0.024 - 0.048: 159 0.048 - 0.072: 65 0.072 - 0.096: 34 0.096 - 0.120: 20 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA VAL K 136 " pdb=" N VAL K 136 " pdb=" C VAL K 136 " pdb=" CB VAL K 136 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA PRO K 462 " pdb=" N PRO K 462 " pdb=" C PRO K 462 " pdb=" CB PRO K 462 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA VAL K 412 " pdb=" N VAL K 412 " pdb=" C VAL K 412 " pdb=" CB VAL K 412 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.43e-01 ... (remaining 635 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 245 " -0.016 5.00e-02 4.00e+02 2.43e-02 9.45e-01 pdb=" N PRO K 246 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO K 246 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO K 246 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 201 " 0.014 5.00e-02 4.00e+02 2.14e-02 7.33e-01 pdb=" N PRO K 202 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO K 202 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO K 202 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 336 " 0.003 2.00e-02 2.50e+03 6.64e-03 4.41e-01 pdb=" C VAL K 336 " -0.011 2.00e-02 2.50e+03 pdb=" O VAL K 336 " 0.004 2.00e-02 2.50e+03 pdb=" N GLY K 337 " 0.004 2.00e-02 2.50e+03 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 247 2.73 - 3.27: 4008 3.27 - 3.82: 6482 3.82 - 4.36: 7028 4.36 - 4.90: 12698 Nonbonded interactions: 30463 Sorted by model distance: nonbonded pdb=" OG1 THR K 299 " pdb=" OD1 ASP K 316 " model vdw 2.190 3.040 nonbonded pdb=" NH2 ARG K 421 " pdb=" O VAL K 469 " model vdw 2.241 3.120 nonbonded pdb=" OD1 ASP K 115 " pdb=" NH2 ARG K 118 " model vdw 2.307 3.120 nonbonded pdb=" O GLY K 35 " pdb=" NZ LYS K 51 " model vdw 2.325 3.120 nonbonded pdb=" OE2 GLU K 214 " pdb=" NH2 ARG K 322 " model vdw 2.336 3.120 ... (remaining 30458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.030 Set scattering table: 0.040 Process input model: 13.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 0.032 3883 Z= 0.197 Angle : 0.491 7.745 5243 Z= 0.271 Chirality : 0.039 0.120 638 Planarity : 0.002 0.024 687 Dihedral : 11.427 88.413 1464 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 2.31 (0.36), residues: 522 helix: 2.48 (0.29), residues: 294 sheet: 0.33 (0.51), residues: 88 loop : 0.38 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.007 0.001 PHE K 195 TYR 0.007 0.001 TYR K 506 ARG 0.001 0.000 ARG K 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.419 Fit side-chains REVERT: K 191 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7343 (pt0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2288 time to fit residues: 9.2636 Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.076112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062875 restraints weight = 11146.005| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.85 r_work: 0.2969 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3883 Z= 0.263 Angle : 0.530 5.529 5243 Z= 0.284 Chirality : 0.041 0.140 638 Planarity : 0.003 0.025 687 Dihedral : 3.741 14.854 552 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: 1.98 (0.35), residues: 522 helix: 2.28 (0.29), residues: 299 sheet: 0.17 (0.57), residues: 72 loop : -0.02 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.012 0.001 PHE K 195 TYR 0.010 0.001 TYR K 199 ARG 0.006 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.426 Fit side-chains REVERT: K 191 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7857 (pt0) REVERT: K 193 MET cc_start: 0.8272 (ptt) cc_final: 0.7751 (ptp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1204 time to fit residues: 4.3491 Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.077781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.064439 restraints weight = 11040.076| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.92 r_work: 0.3005 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3883 Z= 0.149 Angle : 0.456 4.944 5243 Z= 0.246 Chirality : 0.039 0.139 638 Planarity : 0.002 0.024 687 Dihedral : 3.657 13.677 552 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.25 % Allowed : 7.43 % Favored : 92.33 % 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 (0.36), residues: 522 helix: 2.31 (0.29), residues: 299 sheet: -0.01 (0.56), residues: 72 loop : 0.09 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.020 0.002 PHE K 44 TYR 0.008 0.001 TYR K 199 ARG 0.004 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.420 Fit side-chains REVERT: K 506 TYR cc_start: 0.9072 (m-80) cc_final: 0.8830 (m-80) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.1325 time to fit residues: 5.4013 Evaluate side-chains 22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.075412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.061770 restraints weight = 11159.870| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.92 r_work: 0.2945 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3883 Z= 0.286 Angle : 0.527 6.383 5243 Z= 0.277 Chirality : 0.041 0.131 638 Planarity : 0.002 0.020 687 Dihedral : 3.751 14.804 552 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.50 % Allowed : 9.16 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.36), residues: 522 helix: 2.19 (0.29), residues: 299 sheet: -0.31 (0.53), residues: 85 loop : 0.19 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.011 0.001 PHE K 195 TYR 0.010 0.001 TYR K 199 ARG 0.003 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.473 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 23 average time/residue: 0.1254 time to fit residues: 4.3310 Evaluate side-chains 21 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.076608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063479 restraints weight = 11319.244| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.91 r_work: 0.2982 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3883 Z= 0.172 Angle : 0.475 8.011 5243 Z= 0.250 Chirality : 0.039 0.134 638 Planarity : 0.002 0.021 687 Dihedral : 3.679 13.776 552 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.50 % Allowed : 10.64 % Favored : 88.86 % 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: 1.95 (0.36), residues: 522 helix: 2.29 (0.29), residues: 299 sheet: -0.34 (0.53), residues: 85 loop : 0.27 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.016 0.002 PHE K 44 TYR 0.009 0.001 TYR K 199 ARG 0.002 0.000 ARG K 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.467 Fit side-chains REVERT: K 193 MET cc_start: 0.8718 (ppp) cc_final: 0.7574 (ptp) REVERT: K 354 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8791 (tp30) outliers start: 2 outliers final: 0 residues processed: 24 average time/residue: 0.1188 time to fit residues: 4.4039 Evaluate side-chains 22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 0.0470 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.078134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064858 restraints weight = 11013.218| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.95 r_work: 0.3020 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3883 Z= 0.133 Angle : 0.451 6.478 5243 Z= 0.242 Chirality : 0.039 0.139 638 Planarity : 0.002 0.020 687 Dihedral : 3.609 13.056 552 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.99 % Allowed : 11.14 % Favored : 87.87 % 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: 1.99 (0.36), residues: 522 helix: 2.28 (0.29), residues: 302 sheet: -0.30 (0.53), residues: 85 loop : 0.33 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.011 0.001 PHE K 195 TYR 0.007 0.001 TYR K 199 ARG 0.002 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.464 Fit side-chains REVERT: K 354 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8764 (tp30) outliers start: 4 outliers final: 1 residues processed: 28 average time/residue: 0.1334 time to fit residues: 5.3932 Evaluate side-chains 24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 111 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 46 optimal weight: 0.0770 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 51 optimal weight: 0.0980 chunk 12 optimal weight: 6.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.078463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.065409 restraints weight = 11114.246| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.94 r_work: 0.3036 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3883 Z= 0.139 Angle : 0.486 10.011 5243 Z= 0.252 Chirality : 0.039 0.138 638 Planarity : 0.002 0.020 687 Dihedral : 3.629 14.288 552 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.99 % Allowed : 11.88 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.04 (0.36), residues: 522 helix: 2.32 (0.29), residues: 302 sheet: -0.10 (0.54), residues: 80 loop : 0.21 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.007 0.001 PHE K 195 TYR 0.008 0.001 TYR K 199 ARG 0.003 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.421 Fit side-chains REVERT: K 193 MET cc_start: 0.8727 (ppp) cc_final: 0.7549 (ptm) REVERT: K 354 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8747 (tp30) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.1364 time to fit residues: 4.8210 Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 490 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.076076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.062559 restraints weight = 11158.916| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.92 r_work: 0.2963 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3883 Z= 0.296 Angle : 0.568 10.159 5243 Z= 0.293 Chirality : 0.041 0.139 638 Planarity : 0.002 0.020 687 Dihedral : 3.799 19.142 552 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.50 % Allowed : 12.38 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.36), residues: 522 helix: 2.12 (0.29), residues: 303 sheet: -0.42 (0.52), residues: 85 loop : 0.18 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.008 0.001 PHE K 195 TYR 0.010 0.001 TYR K 199 ARG 0.002 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.611 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.1215 time to fit residues: 4.3799 Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 111 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.075003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.061570 restraints weight = 11345.275| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.89 r_work: 0.2935 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3883 Z= 0.322 Angle : 0.554 9.546 5243 Z= 0.291 Chirality : 0.042 0.136 638 Planarity : 0.003 0.023 687 Dihedral : 3.850 19.859 552 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.25 % Allowed : 12.87 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.36), residues: 522 helix: 2.05 (0.29), residues: 302 sheet: -0.49 (0.53), residues: 85 loop : 0.02 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.013 0.002 PHE K 44 TYR 0.011 0.002 TYR K 199 ARG 0.001 0.000 ARG K 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.451 Fit side-chains REVERT: K 193 MET cc_start: 0.8591 (ppp) cc_final: 0.7687 (ptm) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.1450 time to fit residues: 5.1245 Evaluate side-chains 24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 111 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.076865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063806 restraints weight = 11126.465| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.86 r_work: 0.2999 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3883 Z= 0.164 Angle : 0.497 10.551 5243 Z= 0.262 Chirality : 0.039 0.137 638 Planarity : 0.002 0.022 687 Dihedral : 3.697 14.552 552 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.25 % Allowed : 12.62 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.36), residues: 522 helix: 2.18 (0.29), residues: 302 sheet: -0.42 (0.53), residues: 85 loop : 0.14 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.009 0.001 PHE K 195 TYR 0.008 0.001 TYR K 199 ARG 0.002 0.000 ARG K 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.448 Fit side-chains REVERT: K 193 MET cc_start: 0.8635 (ppp) cc_final: 0.7642 (ptm) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.1438 time to fit residues: 5.0775 Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 111 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 49 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.076784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.063512 restraints weight = 10827.462| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.85 r_work: 0.3003 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3883 Z= 0.243 Angle : 0.533 9.723 5243 Z= 0.276 Chirality : 0.041 0.136 638 Planarity : 0.002 0.022 687 Dihedral : 3.724 14.837 552 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.50 % Allowed : 12.62 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.36), residues: 522 helix: 2.16 (0.28), residues: 302 sheet: -0.50 (0.52), residues: 85 loop : 0.11 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.017 0.002 PHE K 44 TYR 0.009 0.001 TYR K 199 ARG 0.001 0.000 ARG K 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1843.27 seconds wall clock time: 32 minutes 45.88 seconds (1965.88 seconds total)