Starting phenix.real_space_refine on Sun Apr 27 23:28:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nf6_9361/04_2025/6nf6_9361.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nf6_9361/04_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_9361/04_2025/6nf6_9361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nf6_9361/04_2025/6nf6_9361.map" model { file = "/net/cci-nas-00/data/ceres_data/6nf6_9361/04_2025/6nf6_9361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nf6_9361/04_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-5669/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: 5.50, per 1000 atoms: 0.83 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: 1.87 Conformation dependent library (CDL) restraints added in 2.3 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: 0.99 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: 2.59 Time building geometry restraints manager: 2.21 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: 3.470 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.920 Find NCS groups from input model: 0.130 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:4.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- 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= 0.303 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 Details of bonding type rmsd hydrogen bonds : bond 0.10775 ( 536) hydrogen bonds : angle 6.03087 ( 1608) covalent geometry : bond 0.00695 ( 6764) covalent geometry : angle 0.97642 ( 9210) *********************** 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 : 0.795 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: 0.2690 time to fit residues: 75.1834 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 : 1.849 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.154957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128922 restraints weight = 7880.880| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.71 r_work: 0.3335 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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= 0.136 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 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 536) hydrogen bonds : angle 4.34429 ( 1608) covalent geometry : bond 0.00295 ( 6764) covalent geometry : angle 0.58246 ( 9210) *********************** 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 : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.6852 (mtpt) cc_final: 0.6014 (mmtm) REVERT: A 260 TYR cc_start: 0.8666 (t80) cc_final: 0.8431 (t80) REVERT: A 424 PHE cc_start: 0.8224 (t80) cc_final: 0.8004 (t80) REVERT: A 546 TYR cc_start: 0.8305 (t80) cc_final: 0.8047 (t80) REVERT: B 254 LYS cc_start: 0.6846 (mtpt) cc_final: 0.6016 (mmtm) REVERT: B 260 TYR cc_start: 0.8659 (t80) cc_final: 0.8422 (t80) REVERT: B 424 PHE cc_start: 0.8190 (t80) cc_final: 0.7970 (t80) REVERT: B 546 TYR cc_start: 0.8303 (t80) cc_final: 0.8040 (t80) outliers start: 10 outliers final: 6 residues processed: 199 average time/residue: 0.3386 time to fit residues: 94.3432 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 : 0.858 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 8.9990 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: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.154404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128166 restraints weight = 8000.772| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.71 r_work: 0.3339 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1945 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= 0.138 Angle : 0.570 6.615 9210 Z= 0.298 Chirality : 0.041 0.214 1110 Planarity : 0.004 0.053 1082 Dihedral : 6.267 47.709 1010 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.51 % Favored : 94.24 % Rotamer: Outliers : 1.93 % Allowed : 15.61 % 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: 1.31 (0.30), residues: 798 helix: 1.73 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.74 (0.53), 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 0.019 0.001 PHE B 320 TYR 0.016 0.001 TYR A 340 ARG 0.001 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 536) hydrogen bonds : angle 4.19523 ( 1608) covalent geometry : bond 0.00306 ( 6764) covalent geometry : angle 0.57034 ( 9210) *********************** 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 201 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.6822 (mtpt) cc_final: 0.6162 (mmtm) REVERT: A 546 TYR cc_start: 0.8310 (t80) cc_final: 0.8043 (t80) REVERT: B 254 LYS cc_start: 0.6843 (mtpt) cc_final: 0.6166 (mmtm) REVERT: B 546 TYR cc_start: 0.8296 (t80) cc_final: 0.8030 (t80) outliers start: 14 outliers final: 10 residues processed: 189 average time/residue: 0.2349 time to fit residues: 60.6734 Evaluate side-chains 177 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 49 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 0.0670 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6122 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.156123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.130046 restraints weight = 8019.365| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.75 r_work: 0.3360 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6764 Z= 0.121 Angle : 0.559 6.205 9210 Z= 0.294 Chirality : 0.041 0.202 1110 Planarity : 0.004 0.051 1082 Dihedral : 6.041 48.527 1010 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.93 % Allowed : 16.44 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.31), residues: 798 helix: 2.10 (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 0.015 0.002 TRP A 127 HIS 0.003 0.001 HIS A 549 PHE 0.011 0.001 PHE A 320 TYR 0.008 0.001 TYR B 340 ARG 0.001 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 536) hydrogen bonds : angle 4.16493 ( 1608) covalent geometry : bond 0.00256 ( 6764) covalent geometry : angle 0.55876 ( 9210) *********************** 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 192 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.886 Fit side-chains REVERT: A 162 ILE cc_start: 0.8851 (mp) cc_final: 0.8378 (pt) REVERT: A 546 TYR cc_start: 0.8307 (t80) cc_final: 0.8005 (t80) REVERT: B 162 ILE cc_start: 0.8893 (mp) cc_final: 0.8402 (pt) REVERT: B 546 TYR cc_start: 0.8300 (t80) cc_final: 0.7993 (t80) outliers start: 14 outliers final: 12 residues processed: 180 average time/residue: 0.1814 time to fit residues: 45.0090 Evaluate side-chains 173 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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: 0.3980 chunk 65 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.153188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126769 restraints weight = 8065.866| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.76 r_work: 0.3324 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6764 Z= 0.161 Angle : 0.600 6.863 9210 Z= 0.318 Chirality : 0.042 0.148 1110 Planarity : 0.004 0.050 1082 Dihedral : 6.174 51.724 1010 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.26 % Favored : 94.49 % Rotamer: Outliers : 2.62 % Allowed : 16.57 % Favored : 80.80 % 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: 1.85 (0.31), residues: 798 helix: 2.11 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.71 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 127 HIS 0.003 0.001 HIS B 549 PHE 0.021 0.001 PHE B 320 TYR 0.018 0.002 TYR A 340 ARG 0.001 0.000 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 536) hydrogen bonds : angle 4.24748 ( 1608) covalent geometry : bond 0.00381 ( 6764) covalent geometry : angle 0.59993 ( 9210) *********************** 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 202 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.717 Fit side-chains REVERT: A 162 ILE cc_start: 0.8836 (mp) cc_final: 0.8382 (pt) REVERT: A 546 TYR cc_start: 0.8327 (t80) cc_final: 0.8027 (t80) REVERT: B 162 ILE cc_start: 0.8874 (mp) cc_final: 0.8405 (pt) REVERT: B 546 TYR cc_start: 0.8313 (t80) cc_final: 0.8013 (t80) outliers start: 19 outliers final: 15 residues processed: 190 average time/residue: 0.1529 time to fit residues: 39.9653 Evaluate side-chains 182 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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: 0.5980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.154504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128251 restraints weight = 7944.725| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.75 r_work: 0.3342 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6764 Z= 0.144 Angle : 0.605 6.559 9210 Z= 0.319 Chirality : 0.042 0.208 1110 Planarity : 0.004 0.049 1082 Dihedral : 6.114 53.309 1010 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.26 % Favored : 94.49 % Rotamer: Outliers : 3.04 % Allowed : 16.85 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.31), residues: 798 helix: 2.20 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.75 (0.52), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 127 HIS 0.003 0.001 HIS B 549 PHE 0.023 0.001 PHE A 320 TYR 0.017 0.001 TYR B 340 ARG 0.001 0.000 ARG B 489 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 536) hydrogen bonds : angle 4.25575 ( 1608) covalent geometry : bond 0.00333 ( 6764) covalent geometry : angle 0.60486 ( 9210) *********************** 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 to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.724 Fit side-chains REVERT: A 162 ILE cc_start: 0.8837 (mp) cc_final: 0.8394 (pt) REVERT: A 546 TYR cc_start: 0.8281 (t80) cc_final: 0.7965 (t80) REVERT: B 162 ILE cc_start: 0.8893 (mp) cc_final: 0.8430 (pt) REVERT: B 546 TYR cc_start: 0.8276 (t80) cc_final: 0.7959 (t80) outliers start: 22 outliers final: 16 residues processed: 186 average time/residue: 0.1702 time to fit residues: 42.6962 Evaluate side-chains 179 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 77 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.155122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128963 restraints weight = 7970.753| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.73 r_work: 0.3344 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2605 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= 0.147 Angle : 0.612 6.735 9210 Z= 0.322 Chirality : 0.042 0.162 1110 Planarity : 0.004 0.049 1082 Dihedral : 6.122 54.915 1010 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.26 % Favored : 94.49 % Rotamer: Outliers : 2.49 % Allowed : 18.78 % 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: 1.94 (0.31), residues: 798 helix: 2.19 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.65 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 101 HIS 0.003 0.001 HIS B 549 PHE 0.023 0.001 PHE B 320 TYR 0.014 0.001 TYR B 340 ARG 0.001 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 536) hydrogen bonds : angle 4.28850 ( 1608) covalent geometry : bond 0.00350 ( 6764) covalent geometry : angle 0.61239 ( 9210) *********************** 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 198 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.770 Fit side-chains REVERT: A 162 ILE cc_start: 0.8846 (mp) cc_final: 0.8383 (pt) REVERT: A 199 MET cc_start: 0.7791 (mmt) cc_final: 0.7294 (mmt) REVERT: A 546 TYR cc_start: 0.8275 (t80) cc_final: 0.7975 (t80) REVERT: B 162 ILE cc_start: 0.8874 (mp) cc_final: 0.8402 (pt) REVERT: B 199 MET cc_start: 0.7794 (mmt) cc_final: 0.7289 (mmt) REVERT: B 546 TYR cc_start: 0.8262 (t80) cc_final: 0.7979 (t80) outliers start: 18 outliers final: 16 residues processed: 188 average time/residue: 0.1550 time to fit residues: 40.7611 Evaluate side-chains 185 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 6 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 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 = 0.3813 r_free = 0.3813 target = 0.158499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132497 restraints weight = 7925.208| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.73 r_work: 0.3404 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2783 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= 0.128 Angle : 0.613 7.545 9210 Z= 0.325 Chirality : 0.041 0.194 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.940 54.319 1010 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.62 % Allowed : 19.20 % 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: 2.03 (0.31), residues: 798 helix: 2.24 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.71 (0.51), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 101 HIS 0.002 0.000 HIS A 549 PHE 0.025 0.001 PHE A 320 TYR 0.022 0.001 TYR A 340 ARG 0.001 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 536) hydrogen bonds : angle 4.32853 ( 1608) covalent geometry : bond 0.00293 ( 6764) covalent geometry : angle 0.61264 ( 9210) *********************** 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 193 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.709 Fit side-chains REVERT: A 162 ILE cc_start: 0.8799 (mp) cc_final: 0.8390 (pt) REVERT: A 223 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: B 162 ILE cc_start: 0.8824 (mp) cc_final: 0.8403 (pt) REVERT: B 223 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: B 546 TYR cc_start: 0.8268 (t80) cc_final: 0.8038 (t80) outliers start: 19 outliers final: 13 residues processed: 185 average time/residue: 0.1564 time to fit residues: 40.2044 Evaluate side-chains 179 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 559 VAL 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 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: 4.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.157230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131292 restraints weight = 8061.323| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.74 r_work: 0.3386 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2801 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= 0.144 Angle : 0.649 9.781 9210 Z= 0.344 Chirality : 0.042 0.180 1110 Planarity : 0.004 0.048 1082 Dihedral : 6.001 55.239 1010 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.89 % Favored : 94.99 % Rotamer: Outliers : 2.62 % Allowed : 20.03 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.31), residues: 798 helix: 2.22 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.61 (0.53), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 101 HIS 0.003 0.001 HIS B 549 PHE 0.026 0.001 PHE B 320 TYR 0.028 0.002 TYR A 426 ARG 0.001 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 536) hydrogen bonds : angle 4.37609 ( 1608) covalent geometry : bond 0.00347 ( 6764) covalent geometry : angle 0.64852 ( 9210) *********************** 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 194 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.731 Fit side-chains REVERT: A 162 ILE cc_start: 0.8827 (mp) cc_final: 0.8403 (pt) REVERT: A 223 GLU cc_start: 0.8117 (mp0) cc_final: 0.7849 (mp0) REVERT: B 162 ILE cc_start: 0.8881 (mp) cc_final: 0.8418 (pt) REVERT: B 223 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7870 (mp0) outliers start: 19 outliers final: 16 residues processed: 185 average time/residue: 0.1617 time to fit residues: 41.3958 Evaluate side-chains 176 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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 559 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A 503 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.157580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131507 restraints weight = 8070.046| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.74 r_work: 0.3372 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6764 Z= 0.157 Angle : 0.661 9.707 9210 Z= 0.352 Chirality : 0.043 0.212 1110 Planarity : 0.004 0.048 1082 Dihedral : 6.076 55.783 1010 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.76 % Allowed : 20.17 % 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: 1.98 (0.31), residues: 798 helix: 2.19 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.54 (0.54), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 180 HIS 0.003 0.001 HIS B 549 PHE 0.028 0.001 PHE A 320 TYR 0.028 0.002 TYR B 426 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 536) hydrogen bonds : angle 4.41858 ( 1608) covalent geometry : bond 0.00381 ( 6764) covalent geometry : angle 0.66064 ( 9210) ********************** 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 182 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.723 Fit side-chains REVERT: A 162 ILE cc_start: 0.8779 (mp) cc_final: 0.8366 (pt) REVERT: A 223 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: B 162 ILE cc_start: 0.8835 (mp) cc_final: 0.8396 (pt) REVERT: B 223 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7828 (mp0) outliers start: 20 outliers final: 16 residues processed: 172 average time/residue: 0.1573 time to fit residues: 37.3141 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 : 0.716 ------------------------------------------------------------------------------- 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 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 559 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.0570 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.176858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.153341 restraints weight = 7596.709| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.63 r_work: 0.3422 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6764 Z= 0.142 Angle : 0.641 9.290 9210 Z= 0.342 Chirality : 0.042 0.190 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.968 55.128 1010 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.49 % Allowed : 20.58 % 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: 2.02 (0.31), residues: 798 helix: 2.20 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.45 (0.53), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 180 HIS 0.002 0.001 HIS B 549 PHE 0.026 0.001 PHE B 320 TYR 0.032 0.002 TYR B 546 ARG 0.002 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 536) hydrogen bonds : angle 4.40491 ( 1608) covalent geometry : bond 0.00338 ( 6764) covalent geometry : angle 0.64149 ( 9210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3882.26 seconds wall clock time: 69 minutes 26.77 seconds (4166.77 seconds total)