Starting phenix.real_space_refine on Tue Feb 13 14:41:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/02_2024/6nf6_9361.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/02_2024/6nf6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/02_2024/6nf6_9361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/02_2024/6nf6_9361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/02_2024/6nf6_9361.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/02_2024/6nf6_9361.pdb" } 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 Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.14, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 2.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.54 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: 1.85 Time building geometry restraints manager: 3.04 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: 99.91 - 106.77: 184 106.77 - 113.63: 3852 113.63 - 120.50: 2826 120.50 - 127.36: 2276 127.36 - 134.22: 72 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 2.440 nonbonded pdb=" O VAL A 338 " pdb=" OG SER A 342 " model vdw 2.309 2.440 nonbonded pdb=" O VAL B 65 " pdb=" OG SER B 69 " model vdw 2.315 2.440 nonbonded pdb=" O VAL A 65 " pdb=" OG SER A 69 " model vdw 2.315 2.440 nonbonded pdb=" O GLN A 190 " pdb=" OG1 THR A 194 " model vdw 2.328 2.440 ... (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 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: 0.350 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: 2.110 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.230 Find NCS groups from input model: 0.350 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.810 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.850 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: 0.1609 time to fit residues: 44.8546 Evaluate side-chains 162 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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: 0.7980 chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 515 HIS A 520 ASN A 523 GLN B 143 ASN B 515 HIS B 520 ASN B 523 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6764 Z= 0.183 Angle : 0.563 6.248 9210 Z= 0.296 Chirality : 0.039 0.131 1110 Planarity : 0.005 0.057 1082 Dihedral : 6.428 51.243 1010 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.21 % Allowed : 12.71 % Favored : 85.08 % 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: 0.49 (0.29), residues: 798 helix: 1.12 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -4.40 (0.53), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 101 HIS 0.003 0.001 HIS A 549 PHE 0.011 0.001 PHE A 178 TYR 0.012 0.002 TYR A 340 ARG 0.001 0.000 ARG B 377 *********************** 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 212 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 196 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.6425 (mtpt) cc_final: 0.5734 (mmtm) REVERT: A 260 TYR cc_start: 0.8677 (t80) cc_final: 0.8333 (t80) REVERT: A 424 PHE cc_start: 0.7935 (t80) cc_final: 0.7692 (t80) REVERT: A 546 TYR cc_start: 0.8157 (t80) cc_final: 0.7873 (t80) REVERT: B 254 LYS cc_start: 0.6397 (mtpt) cc_final: 0.5703 (mmtm) REVERT: B 260 TYR cc_start: 0.8679 (t80) cc_final: 0.8334 (t80) REVERT: B 424 PHE cc_start: 0.7940 (t80) cc_final: 0.7695 (t80) REVERT: B 546 TYR cc_start: 0.8161 (t80) cc_final: 0.7877 (t80) outliers start: 16 outliers final: 10 residues processed: 202 average time/residue: 0.1622 time to fit residues: 44.5406 Evaluate side-chains 193 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 417 SER 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 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 ASN A 523 GLN B 520 ASN B 523 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1956 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= 0.173 Angle : 0.547 6.375 9210 Z= 0.285 Chirality : 0.040 0.229 1110 Planarity : 0.004 0.053 1082 Dihedral : 6.161 47.238 1010 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.73 % Allowed : 15.06 % Favored : 81.22 % 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: 1.52 (0.30), residues: 798 helix: 1.86 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.46 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 101 HIS 0.003 0.001 HIS B 549 PHE 0.019 0.001 PHE B 320 TYR 0.017 0.001 TYR A 340 ARG 0.001 0.000 ARG B 377 *********************** 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 225 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 198 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.6325 (mtpt) cc_final: 0.5896 (mmtm) REVERT: A 546 TYR cc_start: 0.8149 (t80) cc_final: 0.7809 (t80) REVERT: B 254 LYS cc_start: 0.6301 (mtpt) cc_final: 0.5868 (mmtm) REVERT: B 546 TYR cc_start: 0.8150 (t80) cc_final: 0.7809 (t80) outliers start: 27 outliers final: 19 residues processed: 206 average time/residue: 0.1528 time to fit residues: 43.6266 Evaluate side-chains 193 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 174 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 523 GLN 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 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6764 Z= 0.191 Angle : 0.557 6.371 9210 Z= 0.294 Chirality : 0.041 0.200 1110 Planarity : 0.004 0.051 1082 Dihedral : 6.084 48.602 1010 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.59 % Allowed : 16.44 % Favored : 79.97 % 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: 1.81 (0.31), residues: 798 helix: 2.10 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.81 (0.51), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 101 HIS 0.004 0.001 HIS B 549 PHE 0.009 0.001 PHE A 178 TYR 0.008 0.001 TYR A 340 ARG 0.001 0.000 ARG B 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 203 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 177 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ILE cc_start: 0.8652 (mp) cc_final: 0.8207 (pt) REVERT: A 254 LYS cc_start: 0.6356 (mtpt) cc_final: 0.5816 (mmtp) REVERT: A 546 TYR cc_start: 0.8184 (t80) cc_final: 0.7818 (t80) REVERT: B 162 ILE cc_start: 0.8657 (mp) cc_final: 0.8209 (pt) REVERT: B 254 LYS cc_start: 0.6330 (mtpt) cc_final: 0.5781 (mmtp) REVERT: B 546 TYR cc_start: 0.8185 (t80) cc_final: 0.7820 (t80) outliers start: 26 outliers final: 22 residues processed: 183 average time/residue: 0.1758 time to fit residues: 44.1833 Evaluate side-chains 188 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 417 SER 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 57 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 417 SER 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 66 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN B 523 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6764 Z= 0.265 Angle : 0.598 6.874 9210 Z= 0.315 Chirality : 0.042 0.163 1110 Planarity : 0.004 0.050 1082 Dihedral : 6.252 52.954 1010 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.83 % Allowed : 17.27 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.31), residues: 798 helix: 2.12 (0.19), residues: 678 sheet: None (None), residues: 0 loop : -4.60 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 101 HIS 0.005 0.001 HIS B 549 PHE 0.020 0.002 PHE B 320 TYR 0.017 0.002 TYR B 340 ARG 0.001 0.000 ARG A 408 *********************** 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 210 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 TYR cc_start: 0.8239 (t80) cc_final: 0.7872 (t80) REVERT: B 546 TYR cc_start: 0.8241 (t80) cc_final: 0.7876 (t80) outliers start: 35 outliers final: 31 residues processed: 192 average time/residue: 0.2344 time to fit residues: 62.1680 Evaluate side-chains 187 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 156 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 523 GLN 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 57 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 523 GLN 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 26 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.0370 chunk 19 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6764 Z= 0.193 Angle : 0.575 6.145 9210 Z= 0.303 Chirality : 0.040 0.183 1110 Planarity : 0.004 0.050 1082 Dihedral : 6.034 53.229 1010 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.04 % Allowed : 18.51 % Favored : 78.45 % 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: 2.26 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -4.49 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 487 HIS 0.004 0.001 HIS B 549 PHE 0.008 0.001 PHE A 512 TYR 0.017 0.001 TYR A 340 ARG 0.001 0.000 ARG B 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 200 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ILE cc_start: 0.8666 (mp) cc_final: 0.8245 (pt) REVERT: A 546 TYR cc_start: 0.8216 (t80) cc_final: 0.7866 (t80) REVERT: B 162 ILE cc_start: 0.8673 (mp) cc_final: 0.8250 (pt) REVERT: B 546 TYR cc_start: 0.8219 (t80) cc_final: 0.7870 (t80) outliers start: 22 outliers final: 18 residues processed: 186 average time/residue: 0.1686 time to fit residues: 42.3010 Evaluate side-chains 180 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 548 MET 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 8 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 0.0020 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 GLN B 391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2596 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= 0.196 Angle : 0.570 6.564 9210 Z= 0.300 Chirality : 0.040 0.165 1110 Planarity : 0.004 0.049 1082 Dihedral : 5.989 54.324 1010 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.18 % Allowed : 18.92 % Favored : 77.90 % 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: 2.25 (0.31), residues: 798 helix: 2.40 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -4.46 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 101 HIS 0.004 0.001 HIS A 549 PHE 0.018 0.001 PHE A 320 TYR 0.021 0.001 TYR A 340 ARG 0.001 0.000 ARG A 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 197 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.7415 (mmt) cc_final: 0.6881 (mmt) REVERT: A 223 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: A 546 TYR cc_start: 0.8203 (t80) cc_final: 0.7849 (t80) REVERT: B 199 MET cc_start: 0.7420 (mmt) cc_final: 0.6885 (mmt) REVERT: B 223 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: B 546 TYR cc_start: 0.8202 (t80) cc_final: 0.7850 (t80) outliers start: 23 outliers final: 19 residues processed: 183 average time/residue: 0.1514 time to fit residues: 38.3007 Evaluate side-chains 189 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 LEU 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 342 SER Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 57 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 342 SER Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 548 MET 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 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6764 Z= 0.207 Angle : 0.588 6.204 9210 Z= 0.313 Chirality : 0.041 0.169 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.968 55.030 1010 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.01 % Allowed : 17.82 % 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: 2.25 (0.31), residues: 798 helix: 2.39 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.54 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 101 HIS 0.004 0.001 HIS A 549 PHE 0.008 0.001 PHE A 178 TYR 0.018 0.001 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 200 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ILE cc_start: 0.8675 (mp) cc_final: 0.8210 (pt) REVERT: A 223 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: A 546 TYR cc_start: 0.8173 (t80) cc_final: 0.7765 (t80) REVERT: B 162 ILE cc_start: 0.8681 (mp) cc_final: 0.8212 (pt) REVERT: B 223 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: B 546 TYR cc_start: 0.8175 (t80) cc_final: 0.7768 (t80) outliers start: 29 outliers final: 25 residues processed: 184 average time/residue: 0.1750 time to fit residues: 45.0548 Evaluate side-chains 194 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 74 SER 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 342 SER Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 417 SER 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 57 SER Chi-restraints excluded: chain B residue 74 SER 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 342 SER Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 417 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN B 523 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2759 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= 0.212 Angle : 0.607 8.372 9210 Z= 0.322 Chirality : 0.041 0.181 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.978 55.561 1010 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.83 % Allowed : 18.09 % 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: 2.33 (0.31), residues: 798 helix: 2.45 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.49 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 101 HIS 0.004 0.001 HIS A 549 PHE 0.021 0.001 PHE A 320 TYR 0.019 0.001 TYR B 340 ARG 0.001 0.000 ARG A 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 201 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 166 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ILE cc_start: 0.8699 (mp) cc_final: 0.8219 (pt) REVERT: A 223 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: A 546 TYR cc_start: 0.8164 (t80) cc_final: 0.7794 (t80) REVERT: B 162 ILE cc_start: 0.8705 (mp) cc_final: 0.8222 (pt) REVERT: B 223 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: B 546 TYR cc_start: 0.8166 (t80) cc_final: 0.7798 (t80) outliers start: 35 outliers final: 29 residues processed: 183 average time/residue: 0.1537 time to fit residues: 38.9180 Evaluate side-chains 191 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 74 SER 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 226 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 523 GLN 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 57 SER Chi-restraints excluded: chain B residue 74 SER 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 226 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 523 GLN 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 36 optimal weight: 0.0000 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN B 523 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6764 Z= 0.198 Angle : 0.599 8.270 9210 Z= 0.318 Chirality : 0.041 0.190 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.916 55.259 1010 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.56 % Allowed : 18.65 % Favored : 76.80 % 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: 2.32 (0.31), residues: 798 helix: 2.44 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.47 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 101 HIS 0.004 0.001 HIS A 549 PHE 0.008 0.001 PHE B 178 TYR 0.015 0.001 TYR A 340 ARG 0.002 0.000 ARG A 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 197 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ILE cc_start: 0.8679 (mp) cc_final: 0.8207 (pt) REVERT: A 223 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: A 546 TYR cc_start: 0.8164 (t80) cc_final: 0.7782 (t80) REVERT: B 162 ILE cc_start: 0.8688 (mp) cc_final: 0.8212 (pt) REVERT: B 223 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: B 546 TYR cc_start: 0.8164 (t80) cc_final: 0.7785 (t80) outliers start: 33 outliers final: 27 residues processed: 181 average time/residue: 0.1518 time to fit residues: 37.9230 Evaluate side-chains 190 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 74 SER 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 226 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 417 SER 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 57 SER Chi-restraints excluded: chain B residue 74 SER 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 226 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 417 SER 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: 0.7980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 47 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.159680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134331 restraints weight = 7914.563| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.69 r_work: 0.3425 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6764 Z= 0.189 Angle : 0.611 9.522 9210 Z= 0.323 Chirality : 0.041 0.183 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.789 54.135 1010 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.01 % Allowed : 19.48 % Favored : 76.52 % 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: 2.37 (0.31), residues: 798 helix: 2.46 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.37 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 180 HIS 0.004 0.001 HIS B 549 PHE 0.023 0.001 PHE A 320 TYR 0.013 0.001 TYR B 546 ARG 0.002 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1807.42 seconds wall clock time: 33 minutes 23.68 seconds (2003.68 seconds total)