Starting phenix.real_space_refine on Tue Feb 11 21:23:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nf6_9361/02_2025/6nf6_9361.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nf6_9361/02_2025/6nf6_9361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nf6_9361/02_2025/6nf6_9361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nf6_9361/02_2025/6nf6_9361.map" model { file = "/net/cci-nas-00/data/ceres_data/6nf6_9361/02_2025/6nf6_9361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nf6_9361/02_2025/6nf6_9361.cif" } resolution = 3.32 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= 1.000 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 48 5.16 5 C 4428 2.51 5 N 1024 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 6598 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3264 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 12, 'TRANS': 398} Chain breaks: 5 Chain: "B" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3264 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 12, 'TRANS': 398} Chain breaks: 5 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.03, per 1000 atoms: 0.61 Number of scatterers: 6598 At special positions: 0 Unit cell: (91.67, 75.19, 75.19, 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 48 16.00 O 1098 8.00 N 1024 7.00 C 4428 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: 1.66 Conformation dependent library (CDL) restraints added in 923.3 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1548 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 83.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 49 through 78 removed outlier: 3.964A pdb=" N GLY A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 109 Processing helix chain 'A' and resid 127 through 152 Processing helix chain 'A' and resid 162 through 182 removed outlier: 3.724A pdb=" N HIS A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 215 Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.820A pdb=" N GLU A 223 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 280 Proline residue: A 261 - end of helix removed outlier: 3.824A pdb=" N THR A 264 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 Processing helix chain 'A' and resid 334 through 365 removed outlier: 3.812A pdb=" N VAL A 338 " --> pdb=" O TYR A 334 " (cutoff:3.500A) Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 376 through 405 removed outlier: 4.212A pdb=" N GLY A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 437 removed outlier: 3.589A pdb=" N LEU A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 509 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 528 through 559 Proline residue: A 541 - end of helix removed outlier: 3.525A pdb=" N VAL A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 78 Processing helix chain 'B' and resid 83 through 109 Processing helix chain 'B' and resid 127 through 152 Processing helix chain 'B' and resid 162 through 182 removed outlier: 3.724A pdb=" N HIS B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 215 Processing helix chain 'B' and resid 216 through 226 removed outlier: 3.820A pdb=" N GLU B 223 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 280 Proline residue: B 261 - end of helix removed outlier: 3.824A pdb=" N THR B 264 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 328 Processing helix chain 'B' and resid 334 through 365 removed outlier: 3.812A pdb=" N VAL B 338 " --> pdb=" O TYR B 334 " (cutoff:3.500A) Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 376 through 405 removed outlier: 4.212A pdb=" N GLY B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 437 removed outlier: 3.589A pdb=" N LEU B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 509 Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 528 through 559 Proline residue: B 541 - end of helix removed outlier: 3.525A pdb=" N VAL B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1608 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: 2.13 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1136 1.33 - 1.45: 1756 1.45 - 1.57: 3800 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 6764 Sorted by residual: bond pdb=" CAX Y01 A 601 " pdb=" OAH Y01 A 601 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CAX Y01 B 601 " pdb=" OAH Y01 B 601 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C GLN A 112 " pdb=" N PRO A 113 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.12e-02 7.97e+03 6.52e+00 bond pdb=" C GLN B 112 " pdb=" N PRO B 113 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.12e-02 7.97e+03 6.52e+00 bond pdb=" C ASN A 280 " pdb=" N VAL A 281 " ideal model delta sigma weight residual 1.335 1.306 0.029 1.16e-02 7.43e+03 6.31e+00 ... (remaining 6759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 8779 1.99 - 3.97: 337 3.97 - 5.96: 68 5.96 - 7.95: 20 7.95 - 9.93: 6 Bond angle restraints: 9210 Sorted by residual: angle pdb=" CA GLY B 528 " pdb=" C GLY B 528 " pdb=" O GLY B 528 " ideal model delta sigma weight residual 122.22 119.74 2.48 6.50e-01 2.37e+00 1.46e+01 angle pdb=" CA GLY A 528 " pdb=" C GLY A 528 " pdb=" O GLY A 528 " ideal model delta sigma weight residual 122.22 119.74 2.48 6.50e-01 2.37e+00 1.46e+01 angle pdb=" C MET B 277 " pdb=" N TRP B 278 " pdb=" CA TRP B 278 " ideal model delta sigma weight residual 122.11 116.69 5.42 1.64e+00 3.72e-01 1.09e+01 angle pdb=" C MET A 277 " pdb=" N TRP A 278 " pdb=" CA TRP A 278 " ideal model delta sigma weight residual 122.11 116.69 5.42 1.64e+00 3.72e-01 1.09e+01 angle pdb=" CA TRP A 101 " pdb=" CB TRP A 101 " pdb=" CG TRP A 101 " ideal model delta sigma weight residual 113.60 107.43 6.17 1.90e+00 2.77e-01 1.06e+01 ... (remaining 9205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 3446 16.85 - 33.70: 434 33.70 - 50.55: 90 50.55 - 67.39: 18 67.39 - 84.24: 10 Dihedral angle restraints: 3998 sinusoidal: 1600 harmonic: 2398 Sorted by residual: dihedral pdb=" CA ALA B 331 " pdb=" C ALA B 331 " pdb=" N PRO B 332 " pdb=" CA PRO B 332 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ALA A 331 " pdb=" C ALA A 331 " pdb=" N PRO A 332 " pdb=" CA PRO A 332 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASN B 280 " pdb=" C ASN B 280 " pdb=" N VAL B 281 " pdb=" CA VAL B 281 " ideal model delta harmonic sigma weight residual 180.00 155.48 24.52 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 3995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1002 0.093 - 0.185: 98 0.185 - 0.278: 6 0.278 - 0.370: 2 0.370 - 0.463: 2 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CBG Y01 A 601 " pdb=" CAQ Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CBG Y01 B 601 " pdb=" CAQ Y01 B 601 " pdb=" CBD Y01 B 601 " pdb=" CBI Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.79 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CBH Y01 B 601 " pdb=" CAT Y01 B 601 " pdb=" CAZ Y01 B 601 " pdb=" CBF Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.57 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1107 not shown) Planarity restraints: 1082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 305 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO A 306 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 306 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 306 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 305 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO B 306 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 306 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 306 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 260 " 0.039 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO B 261 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.033 5.00e-02 4.00e+02 ... (remaining 1079 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2049 2.83 - 3.35: 6386 3.35 - 3.86: 11322 3.86 - 4.38: 12375 4.38 - 4.90: 22258 Nonbonded interactions: 54390 Sorted by model distance: nonbonded pdb=" O VAL B 338 " pdb=" OG SER B 342 " model vdw 2.309 3.040 nonbonded pdb=" O VAL A 338 " pdb=" OG SER A 342 " model vdw 2.309 3.040 nonbonded pdb=" O VAL B 65 " pdb=" OG SER B 69 " model vdw 2.315 3.040 nonbonded pdb=" O VAL A 65 " pdb=" OG SER A 69 " model vdw 2.315 3.040 nonbonded pdb=" O GLN A 190 " pdb=" OG1 THR A 194 " model vdw 2.328 3.040 ... (remaining 54385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.790 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.007 0.094 6764 Z= 0.445 Angle : 0.976 9.934 9210 Z= 0.513 Chirality : 0.060 0.463 1110 Planarity : 0.008 0.067 1082 Dihedral : 15.515 84.243 2450 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.51 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % 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: -2.74 (0.24), residues: 798 helix: -1.19 (0.15), residues: 660 sheet: None (None), residues: 0 loop : -4.17 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 101 HIS 0.008 0.001 HIS A 549 PHE 0.016 0.002 PHE A 71 TYR 0.016 0.002 TYR A 275 ARG 0.002 0.001 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 LYS cc_start: 0.6887 (tttt) cc_final: 0.6623 (tmtt) REVERT: A 254 LYS cc_start: 0.6552 (mtpt) cc_final: 0.5822 (mmtm) REVERT: A 260 TYR cc_start: 0.8620 (t80) cc_final: 0.8217 (t80) REVERT: A 335 GLN cc_start: 0.8292 (mp10) cc_final: 0.8081 (mp10) REVERT: A 424 PHE cc_start: 0.7969 (t80) cc_final: 0.7662 (t80) REVERT: B 184 LYS cc_start: 0.6878 (tttt) cc_final: 0.6624 (tmtt) REVERT: B 254 LYS cc_start: 0.6525 (mtpt) cc_final: 0.5792 (mmtm) REVERT: B 260 TYR cc_start: 0.8626 (t80) cc_final: 0.8219 (t80) REVERT: B 335 GLN cc_start: 0.8297 (mp10) cc_final: 0.8083 (mp10) REVERT: B 424 PHE cc_start: 0.7974 (t80) cc_final: 0.7669 (t80) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1627 time to fit residues: 45.2192 Evaluate side-chains 162 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS B 515 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.154915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.128893 restraints weight = 7880.205| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.71 r_work: 0.3334 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6764 Z= 0.192 Angle : 0.582 6.445 9210 Z= 0.309 Chirality : 0.040 0.134 1110 Planarity : 0.005 0.057 1082 Dihedral : 6.553 50.680 1010 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.38 % Allowed : 13.26 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.29), residues: 798 helix: 1.03 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -4.44 (0.53), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 101 HIS 0.006 0.001 HIS A 549 PHE 0.012 0.001 PHE A 178 TYR 0.013 0.002 TYR B 340 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.6937 (mtpt) cc_final: 0.6107 (mmtm) REVERT: A 260 TYR cc_start: 0.8636 (t80) cc_final: 0.8417 (t80) REVERT: A 424 PHE cc_start: 0.8223 (t80) cc_final: 0.8011 (t80) REVERT: A 546 TYR cc_start: 0.8313 (t80) cc_final: 0.8055 (t80) REVERT: B 254 LYS cc_start: 0.6934 (mtpt) cc_final: 0.6108 (mmtm) REVERT: B 260 TYR cc_start: 0.8631 (t80) cc_final: 0.8410 (t80) REVERT: B 424 PHE cc_start: 0.8190 (t80) cc_final: 0.7976 (t80) REVERT: B 546 TYR cc_start: 0.8307 (t80) cc_final: 0.8046 (t80) outliers start: 10 outliers final: 6 residues processed: 199 average time/residue: 0.1668 time to fit residues: 45.0431 Evaluate side-chains 184 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128012 restraints weight = 8003.753| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.71 r_work: 0.3337 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6764 Z= 0.201 Angle : 0.573 6.677 9210 Z= 0.300 Chirality : 0.041 0.222 1110 Planarity : 0.004 0.053 1082 Dihedral : 6.282 47.761 1010 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.07 % Allowed : 15.47 % Favored : 82.46 % 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: 1.30 (0.30), residues: 798 helix: 1.72 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.74 (0.54), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 101 HIS 0.004 0.001 HIS B 549 PHE 0.020 0.001 PHE B 320 TYR 0.016 0.001 TYR A 340 ARG 0.001 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.6822 (mtpt) cc_final: 0.6157 (mmtm) REVERT: A 546 TYR cc_start: 0.8313 (t80) cc_final: 0.8045 (t80) REVERT: B 254 LYS cc_start: 0.6847 (mtpt) cc_final: 0.6165 (mmtm) REVERT: B 546 TYR cc_start: 0.8298 (t80) cc_final: 0.8030 (t80) outliers start: 15 outliers final: 11 residues processed: 189 average time/residue: 0.1696 time to fit residues: 43.7564 Evaluate side-chains 177 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.155070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128922 restraints weight = 8043.456| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.75 r_work: 0.3362 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6764 Z= 0.183 Angle : 0.565 6.366 9210 Z= 0.298 Chirality : 0.041 0.195 1110 Planarity : 0.004 0.051 1082 Dihedral : 6.108 49.027 1010 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.51 % Favored : 94.24 % Rotamer: Outliers : 1.93 % Allowed : 16.57 % Favored : 81.49 % 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 (0.31), residues: 798 helix: 2.05 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.73 (0.52), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 101 HIS 0.003 0.001 HIS A 549 PHE 0.011 0.001 PHE A 320 TYR 0.008 0.001 TYR B 418 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.784 Fit side-chains REVERT: A 162 ILE cc_start: 0.8821 (mp) cc_final: 0.8368 (pt) REVERT: A 546 TYR cc_start: 0.8311 (t80) cc_final: 0.8021 (t80) REVERT: B 162 ILE cc_start: 0.8863 (mp) cc_final: 0.8392 (pt) REVERT: B 546 TYR cc_start: 0.8297 (t80) cc_final: 0.8006 (t80) outliers start: 14 outliers final: 12 residues processed: 182 average time/residue: 0.1726 time to fit residues: 42.9466 Evaluate side-chains 178 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 0.0070 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.157493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131235 restraints weight = 7959.741| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.74 r_work: 0.3380 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6764 Z= 0.183 Angle : 0.569 6.398 9210 Z= 0.302 Chirality : 0.040 0.146 1110 Planarity : 0.004 0.050 1082 Dihedral : 6.000 50.256 1010 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.89 % Favored : 94.86 % Rotamer: Outliers : 2.62 % Allowed : 16.30 % Favored : 81.08 % 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: 1.99 (0.31), residues: 798 helix: 2.22 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.73 (0.51), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 127 HIS 0.002 0.000 HIS A 549 PHE 0.021 0.001 PHE A 320 TYR 0.019 0.001 TYR A 340 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.685 Fit side-chains REVERT: A 162 ILE cc_start: 0.8836 (mp) cc_final: 0.8364 (pt) REVERT: A 199 MET cc_start: 0.7822 (mmt) cc_final: 0.7318 (mmt) REVERT: A 546 TYR cc_start: 0.8314 (t80) cc_final: 0.7992 (t80) REVERT: B 162 ILE cc_start: 0.8865 (mp) cc_final: 0.8391 (pt) REVERT: B 199 MET cc_start: 0.7793 (mmt) cc_final: 0.7282 (mmt) REVERT: B 546 TYR cc_start: 0.8307 (t80) cc_final: 0.7998 (t80) outliers start: 19 outliers final: 15 residues processed: 184 average time/residue: 0.1611 time to fit residues: 40.4160 Evaluate side-chains 175 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.155700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129293 restraints weight = 7935.105| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.75 r_work: 0.3357 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6764 Z= 0.208 Angle : 0.592 6.547 9210 Z= 0.313 Chirality : 0.042 0.210 1110 Planarity : 0.004 0.049 1082 Dihedral : 6.043 52.241 1010 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.04 % Allowed : 18.09 % Favored : 78.87 % 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: 2.06 (0.31), residues: 798 helix: 2.26 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.70 (0.52), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 487 HIS 0.003 0.001 HIS B 549 PHE 0.010 0.001 PHE B 178 TYR 0.016 0.001 TYR B 546 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.743 Fit side-chains REVERT: A 162 ILE cc_start: 0.8767 (mp) cc_final: 0.8327 (pt) REVERT: A 223 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: A 546 TYR cc_start: 0.8275 (t80) cc_final: 0.7956 (t80) REVERT: B 162 ILE cc_start: 0.8812 (mp) cc_final: 0.8351 (pt) REVERT: B 223 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: B 546 TYR cc_start: 0.8269 (t80) cc_final: 0.7926 (t80) outliers start: 22 outliers final: 16 residues processed: 187 average time/residue: 0.1710 time to fit residues: 43.2948 Evaluate side-chains 181 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.156520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130170 restraints weight = 7954.555| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.75 r_work: 0.3357 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6764 Z= 0.224 Angle : 0.606 6.716 9210 Z= 0.319 Chirality : 0.041 0.161 1110 Planarity : 0.004 0.049 1082 Dihedral : 6.060 53.739 1010 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.76 % Favored : 94.99 % Rotamer: Outliers : 3.31 % Allowed : 17.96 % Favored : 78.73 % 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: 2.05 (0.31), residues: 798 helix: 2.28 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.71 (0.51), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 127 HIS 0.003 0.001 HIS A 549 PHE 0.024 0.001 PHE A 320 TYR 0.012 0.001 TYR B 546 ARG 0.001 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.913 Fit side-chains REVERT: A 162 ILE cc_start: 0.8833 (mp) cc_final: 0.8355 (pt) REVERT: A 223 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: B 162 ILE cc_start: 0.8862 (mp) cc_final: 0.8366 (pt) REVERT: B 223 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7452 (mp0) outliers start: 24 outliers final: 18 residues processed: 185 average time/residue: 0.1582 time to fit residues: 41.3418 Evaluate side-chains 184 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 6 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 overall best weight: 0.4166 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.163757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138314 restraints weight = 7877.802| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.72 r_work: 0.3428 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6764 Z= 0.189 Angle : 0.621 8.128 9210 Z= 0.327 Chirality : 0.041 0.192 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.845 52.832 1010 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.35 % Allowed : 19.48 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.31), residues: 798 helix: 2.30 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.73 (0.50), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 101 HIS 0.002 0.000 HIS A 549 PHE 0.024 0.001 PHE B 320 TYR 0.028 0.002 TYR B 546 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.701 Fit side-chains REVERT: A 162 ILE cc_start: 0.8827 (mp) cc_final: 0.8425 (pt) REVERT: A 223 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: B 162 ILE cc_start: 0.8849 (mp) cc_final: 0.8428 (pt) REVERT: B 223 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7817 (mp0) outliers start: 17 outliers final: 11 residues processed: 181 average time/residue: 0.1549 time to fit residues: 38.9274 Evaluate side-chains 180 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 0.0670 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN B 429 GLN B 503 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.160031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134154 restraints weight = 8057.538| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.76 r_work: 0.3425 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6764 Z= 0.214 Angle : 0.634 9.881 9210 Z= 0.337 Chirality : 0.041 0.172 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.884 53.646 1010 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.49 % Allowed : 20.44 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.31), residues: 798 helix: 2.30 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.70 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 101 HIS 0.002 0.001 HIS A 219 PHE 0.026 0.001 PHE A 320 TYR 0.023 0.002 TYR B 546 ARG 0.001 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.693 Fit side-chains REVERT: A 162 ILE cc_start: 0.8825 (mp) cc_final: 0.8405 (pt) REVERT: A 223 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: B 162 ILE cc_start: 0.8857 (mp) cc_final: 0.8419 (pt) REVERT: B 223 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7782 (mp0) outliers start: 18 outliers final: 14 residues processed: 179 average time/residue: 0.1513 time to fit residues: 37.5852 Evaluate side-chains 176 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.159728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133623 restraints weight = 8054.723| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.77 r_work: 0.3398 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6764 Z= 0.222 Angle : 0.643 9.689 9210 Z= 0.342 Chirality : 0.042 0.206 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.911 53.964 1010 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.62 % Allowed : 20.72 % Favored : 76.66 % 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: 2.09 (0.31), residues: 798 helix: 2.29 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.60 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 180 HIS 0.002 0.001 HIS A 549 PHE 0.027 0.001 PHE B 320 TYR 0.024 0.002 TYR B 546 ARG 0.002 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.734 Fit side-chains REVERT: A 162 ILE cc_start: 0.8808 (mp) cc_final: 0.8384 (pt) REVERT: A 223 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: B 162 ILE cc_start: 0.8839 (mp) cc_final: 0.8402 (pt) REVERT: B 223 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7766 (mp0) outliers start: 19 outliers final: 14 residues processed: 159 average time/residue: 0.1608 time to fit residues: 35.1149 Evaluate side-chains 166 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.161677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135669 restraints weight = 8034.378| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.73 r_work: 0.3421 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6764 Z= 0.220 Angle : 0.629 9.113 9210 Z= 0.336 Chirality : 0.042 0.195 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.898 53.682 1010 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.76 % Allowed : 20.30 % Favored : 76.93 % 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: 2.13 (0.31), residues: 798 helix: 2.32 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -4.48 (0.48), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.002 0.001 HIS A 549 PHE 0.029 0.001 PHE A 320 TYR 0.023 0.002 TYR B 546 ARG 0.001 0.000 ARG A 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3407.03 seconds wall clock time: 61 minutes 22.73 seconds (3682.73 seconds total)