Starting phenix.real_space_refine on Tue Feb 11 03:12:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xop_33355/02_2025/7xop_33355.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xop_33355/02_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_33355/02_2025/7xop_33355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xop_33355/02_2025/7xop_33355.map" model { file = "/net/cci-nas-00/data/ceres_data/7xop_33355/02_2025/7xop_33355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xop_33355/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.02, per 1000 atoms: 0.78 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: 0.98 Conformation dependent library (CDL) restraints added in 529.3 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: 0.40 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: 1.11 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: 1.110 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: 13.910 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.320 ------------------------------------------------------------------------------- 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 : 0.464 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: 0.2319 time to fit residues: 9.3927 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 : 0.480 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062880 restraints weight = 11146.008| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.85 r_work: 0.2970 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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 : 0.441 Fit side-chains REVERT: K 193 MET cc_start: 0.8251 (ptt) cc_final: 0.7745 (ptp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1319 time to fit residues: 4.7341 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 : 0.457 ------------------------------------------------------------------------------- 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: 7.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.076896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063615 restraints weight = 11059.575| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.89 r_work: 0.2979 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3883 Z= 0.193 Angle : 0.476 4.960 5243 Z= 0.256 Chirality : 0.040 0.137 638 Planarity : 0.002 0.024 687 Dihedral : 3.693 14.229 552 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.25 % Allowed : 7.67 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.36), residues: 522 helix: 2.26 (0.29), residues: 299 sheet: -0.04 (0.56), residues: 72 loop : 0.03 (0.49), 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 0.009 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 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.395 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.1203 time to fit residues: 4.5959 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 : 0.419 ------------------------------------------------------------------------------- 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: 5.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.077039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.063689 restraints weight = 11087.779| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.89 r_work: 0.2985 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3883 Z= 0.179 Angle : 0.478 6.398 5243 Z= 0.254 Chirality : 0.040 0.134 638 Planarity : 0.002 0.021 687 Dihedral : 3.676 14.041 552 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.25 % Allowed : 8.91 % Favored : 90.84 % 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: 1.86 (0.36), residues: 522 helix: 2.28 (0.29), residues: 299 sheet: -0.48 (0.51), residues: 91 loop : 0.17 (0.54), residues: 132 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 0.008 0.001 TYR K 199 ARG 0.002 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 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.437 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.1416 time to fit residues: 5.0661 Evaluate side-chains 23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.076005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.062692 restraints weight = 11357.537| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.90 r_work: 0.2964 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3883 Z= 0.248 Angle : 0.511 8.163 5243 Z= 0.267 Chirality : 0.040 0.132 638 Planarity : 0.002 0.021 687 Dihedral : 3.726 14.608 552 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.74 % Allowed : 10.15 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.36), residues: 522 helix: 2.26 (0.29), residues: 299 sheet: -0.39 (0.53), residues: 85 loop : 0.18 (0.52), residues: 138 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 0.009 0.001 TYR K 199 ARG 0.002 0.000 ARG K 18 *********************** 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: 3 poor density : 22 time to evaluate : 0.436 Fit side-chains REVERT: K 193 MET cc_start: 0.8698 (ppp) cc_final: 0.7686 (ptm) REVERT: K 520 MET cc_start: 0.8260 (mtt) cc_final: 0.7770 (mtt) outliers start: 3 outliers final: 0 residues processed: 24 average time/residue: 0.1330 time to fit residues: 4.5303 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 : 0.411 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 4 optimal weight: 0.0370 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.076320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063141 restraints weight = 11096.164| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.86 r_work: 0.2978 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1682 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= 0.201 Angle : 0.485 6.391 5243 Z= 0.256 Chirality : 0.040 0.134 638 Planarity : 0.002 0.021 687 Dihedral : 3.691 14.161 552 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.74 % Allowed : 10.64 % Favored : 88.61 % 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: 1.89 (0.36), residues: 522 helix: 2.26 (0.29), residues: 299 sheet: -0.40 (0.53), residues: 85 loop : 0.22 (0.53), residues: 138 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 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 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.436 Fit side-chains REVERT: K 193 MET cc_start: 0.8714 (ppp) cc_final: 0.7635 (ptm) REVERT: K 520 MET cc_start: 0.8307 (mtt) cc_final: 0.7906 (mtt) outliers start: 3 outliers final: 0 residues processed: 26 average time/residue: 0.1360 time to fit residues: 5.0436 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 : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.077649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.064499 restraints weight = 11164.021| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.89 r_work: 0.3009 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3883 Z= 0.145 Angle : 0.451 5.565 5243 Z= 0.243 Chirality : 0.039 0.140 638 Planarity : 0.002 0.020 687 Dihedral : 3.629 12.943 552 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 1.96 (0.36), residues: 522 helix: 2.26 (0.29), residues: 302 sheet: -0.19 (0.53), residues: 80 loop : 0.20 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.006 0.001 PHE K 195 TYR 0.008 0.001 TYR K 199 ARG 0.002 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 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.405 Fit side-chains REVERT: K 193 MET cc_start: 0.8783 (ppp) cc_final: 0.7659 (ptm) REVERT: K 520 MET cc_start: 0.8199 (mtt) cc_final: 0.7879 (mtt) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.1413 time to fit residues: 5.1516 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 : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0020 chunk 51 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.078340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.065351 restraints weight = 11066.278| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.87 r_work: 0.3033 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3883 Z= 0.137 Angle : 0.475 7.278 5243 Z= 0.251 Chirality : 0.039 0.138 638 Planarity : 0.002 0.020 687 Dihedral : 3.628 13.858 552 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: 1.96 (0.36), residues: 522 helix: 2.28 (0.29), residues: 303 sheet: -0.12 (0.54), residues: 80 loop : 0.06 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.015 0.001 PHE K 44 TYR 0.008 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 24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.463 Fit side-chains REVERT: K 193 MET cc_start: 0.8793 (ppp) cc_final: 0.7643 (ptm) REVERT: K 520 MET cc_start: 0.8000 (mtt) cc_final: 0.7746 (mtt) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.1567 time to fit residues: 5.0599 Evaluate side-chains 23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.075137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.061397 restraints weight = 11413.697| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.93 r_work: 0.2932 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3883 Z= 0.344 Angle : 0.560 6.955 5243 Z= 0.292 Chirality : 0.042 0.134 638 Planarity : 0.003 0.022 687 Dihedral : 3.765 16.370 552 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.25 % Allowed : 13.12 % Favored : 86.63 % 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: 1.74 (0.36), residues: 522 helix: 2.16 (0.29), residues: 302 sheet: -0.55 (0.52), residues: 85 loop : 0.12 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.009 0.001 PHE K 195 TYR 0.011 0.001 TYR K 199 ARG 0.002 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 23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.426 Fit side-chains REVERT: K 193 MET cc_start: 0.8803 (ppp) cc_final: 0.7735 (ptm) REVERT: K 520 MET cc_start: 0.8658 (mtt) cc_final: 0.8347 (mtt) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.1297 time to fit residues: 4.4531 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 : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.0170 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 0.0170 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.076706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063494 restraints weight = 11163.487| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.86 r_work: 0.2986 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3883 Z= 0.165 Angle : 0.485 6.626 5243 Z= 0.257 Chirality : 0.039 0.136 638 Planarity : 0.002 0.021 687 Dihedral : 3.668 15.078 552 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: 1.90 (0.36), residues: 522 helix: 2.30 (0.29), residues: 300 sheet: -0.31 (0.53), residues: 80 loop : 0.03 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.008 0.001 PHE K 195 TYR 0.008 0.001 TYR K 199 ARG 0.002 0.000 ARG K 18 ********************** 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 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 Fit side-chains REVERT: K 193 MET cc_start: 0.8808 (ppp) cc_final: 0.8549 (ppp) REVERT: K 520 MET cc_start: 0.8250 (mtt) cc_final: 0.7978 (mtt) outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.1436 time to fit residues: 5.0700 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 : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 8 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.076265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.062497 restraints weight = 11011.446| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.94 r_work: 0.2975 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3883 Z= 0.311 Angle : 0.534 5.891 5243 Z= 0.282 Chirality : 0.042 0.135 638 Planarity : 0.002 0.022 687 Dihedral : 3.755 15.985 552 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.25 % Allowed : 13.37 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.36), residues: 522 helix: 2.20 (0.28), residues: 299 sheet: -0.64 (0.52), residues: 85 loop : 0.08 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.015 0.002 PHE K 44 TYR 0.011 0.001 TYR K 199 ARG 0.002 0.000 ARG K 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1839.59 seconds wall clock time: 33 minutes 28.12 seconds (2008.12 seconds total)