Starting phenix.real_space_refine on Thu Dec 7 16:13:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6e_12053/12_2023/7b6e_12053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6e_12053/12_2023/7b6e_12053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6e_12053/12_2023/7b6e_12053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6e_12053/12_2023/7b6e_12053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6e_12053/12_2023/7b6e_12053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6e_12053/12_2023/7b6e_12053.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 13 5.16 5 C 1406 2.51 5 N 389 2.21 5 O 397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A GLU 649": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2205 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2205 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 4, 'TRANS': 264} Chain breaks: 1 Time building chain proxies: 1.79, per 1000 atoms: 0.81 Number of scatterers: 2205 At special positions: 0 Unit cell: (63.648, 73.632, 92.352, 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 13 16.00 O 397 8.00 N 389 7.00 C 1406 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: 0.94 Conformation dependent library (CDL) restraints added in 407.1 milliseconds 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 522 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 86.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 355 through 384 removed outlier: 4.194A pdb=" N HIS A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 425 through 438 removed outlier: 4.158A pdb=" N PHE A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 456 Processing helix chain 'A' and resid 461 through 477 Processing helix chain 'A' and resid 483 through 500 removed outlier: 3.762A pdb=" N THR A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 removed outlier: 4.176A pdb=" N ALA A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.905A pdb=" N ASN A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 557 removed outlier: 3.726A pdb=" N THR A 556 " --> pdb=" O CYS A 552 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 579 removed outlier: 4.874A pdb=" N ARG A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 598 removed outlier: 3.665A pdb=" N ARG A 598 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 614 removed outlier: 4.015A pdb=" N GLU A 604 " --> pdb=" O TRP A 600 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 removed outlier: 4.487A pdb=" N ALA A 624 " --> pdb=" O GLN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 661 165 hydrogen bonds defined for protein. 495 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: 0.56 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 691 1.34 - 1.46: 378 1.46 - 1.57: 1162 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 2252 Sorted by residual: bond pdb=" CB PRO A 559 " pdb=" CG PRO A 559 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.59e+00 bond pdb=" CG PRO A 559 " pdb=" CD PRO A 559 " ideal model delta sigma weight residual 1.503 1.542 -0.039 3.40e-02 8.65e+02 1.32e+00 bond pdb=" CB PHE A 436 " pdb=" CG PHE A 436 " ideal model delta sigma weight residual 1.502 1.476 0.026 2.30e-02 1.89e+03 1.30e+00 bond pdb=" N TRP A 600 " pdb=" CA TRP A 600 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.20e+00 bond pdb=" CG LEU A 468 " pdb=" CD2 LEU A 468 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 ... (remaining 2247 not shown) Histogram of bond angle deviations from ideal: 96.90 - 104.31: 21 104.31 - 111.73: 947 111.73 - 119.14: 834 119.14 - 126.56: 1211 126.56 - 133.97: 24 Bond angle restraints: 3037 Sorted by residual: angle pdb=" CA PRO A 559 " pdb=" N PRO A 559 " pdb=" CD PRO A 559 " ideal model delta sigma weight residual 112.00 102.11 9.89 1.40e+00 5.10e-01 4.99e+01 angle pdb=" C LEU A 434 " pdb=" N TYR A 435 " pdb=" CA TYR A 435 " ideal model delta sigma weight residual 121.58 113.58 8.00 1.95e+00 2.63e-01 1.68e+01 angle pdb=" CA LEU A 468 " pdb=" CB LEU A 468 " pdb=" CG LEU A 468 " ideal model delta sigma weight residual 116.30 130.26 -13.96 3.50e+00 8.16e-02 1.59e+01 angle pdb=" CA ARG A 508 " pdb=" CB ARG A 508 " pdb=" CG ARG A 508 " ideal model delta sigma weight residual 114.10 122.05 -7.95 2.00e+00 2.50e-01 1.58e+01 angle pdb=" C ALA A 467 " pdb=" N LEU A 468 " pdb=" CA LEU A 468 " ideal model delta sigma weight residual 120.31 115.02 5.29 1.52e+00 4.33e-01 1.21e+01 ... (remaining 3032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 1143 15.16 - 30.32: 169 30.32 - 45.48: 35 45.48 - 60.64: 2 60.64 - 75.79: 4 Dihedral angle restraints: 1353 sinusoidal: 544 harmonic: 809 Sorted by residual: dihedral pdb=" CA ARG A 598 " pdb=" C ARG A 598 " pdb=" N GLU A 599 " pdb=" CA GLU A 599 " ideal model delta harmonic sigma weight residual -180.00 -145.66 -34.34 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA SER A 538 " pdb=" C SER A 538 " pdb=" N ASP A 539 " pdb=" CA ASP A 539 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLN A 482 " pdb=" C GLN A 482 " pdb=" N ARG A 483 " pdb=" CA ARG A 483 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 1350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 199 0.041 - 0.082: 93 0.082 - 0.123: 23 0.123 - 0.165: 6 0.165 - 0.206: 5 Chirality restraints: 326 Sorted by residual: chirality pdb=" CA GLN A 529 " pdb=" N GLN A 529 " pdb=" C GLN A 529 " pdb=" CB GLN A 529 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ARG A 508 " pdb=" N ARG A 508 " pdb=" C ARG A 508 " pdb=" CB ARG A 508 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA GLU A 469 " pdb=" N GLU A 469 " pdb=" C GLU A 469 " pdb=" CB GLU A 469 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 323 not shown) Planarity restraints: 388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 558 " 0.075 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO A 559 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 559 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 559 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 547 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" CD GLU A 547 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 547 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 547 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 508 " -0.039 9.50e-02 1.11e+02 2.36e-02 3.33e+00 pdb=" NE ARG A 508 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 508 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 508 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 508 " 0.009 2.00e-02 2.50e+03 ... (remaining 385 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 90 2.68 - 3.24: 2676 3.24 - 3.79: 3824 3.79 - 4.35: 5131 4.35 - 4.90: 7212 Nonbonded interactions: 18933 Sorted by model distance: nonbonded pdb=" O ALA A 471 " pdb=" OG SER A 474 " model vdw 2.129 2.440 nonbonded pdb=" OE1 GLN A 482 " pdb=" NZ LYS A 484 " model vdw 2.161 2.520 nonbonded pdb=" O CYS A 516 " pdb=" OG1 THR A 519 " model vdw 2.178 2.440 nonbonded pdb=" O GLU A 382 " pdb=" OG1 THR A 385 " model vdw 2.191 2.440 nonbonded pdb=" O ALA A 612 " pdb=" N TYR A 616 " model vdw 2.203 2.520 ... (remaining 18928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 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: 13.580 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 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 : 0.005 0.063 2252 Z= 0.309 Angle : 1.026 13.963 3037 Z= 0.575 Chirality : 0.053 0.206 326 Planarity : 0.007 0.108 388 Dihedral : 15.044 75.794 831 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 36.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -3.88 (0.43), residues: 265 helix: -2.02 (0.29), residues: 225 sheet: None (None), residues: 0 loop : -4.52 (0.69), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 600 HIS 0.007 0.002 HIS A 561 PHE 0.015 0.003 PHE A 628 TYR 0.026 0.002 TYR A 435 ARG 0.031 0.002 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1963 time to fit residues: 6.8852 Evaluate side-chains 24 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2252 Z= 0.222 Angle : 0.865 11.941 3037 Z= 0.445 Chirality : 0.047 0.174 326 Planarity : 0.005 0.042 388 Dihedral : 6.931 25.669 306 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % 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: -2.80 (0.46), residues: 265 helix: -1.26 (0.31), residues: 224 sheet: None (None), residues: 0 loop : -4.33 (0.70), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 600 HIS 0.004 0.001 HIS A 561 PHE 0.031 0.003 PHE A 628 TYR 0.024 0.002 TYR A 435 ARG 0.008 0.001 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1735 time to fit residues: 6.4785 Evaluate side-chains 23 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.296 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2252 Z= 0.212 Angle : 0.892 13.462 3037 Z= 0.450 Chirality : 0.046 0.186 326 Planarity : 0.004 0.040 388 Dihedral : 6.751 26.230 306 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % 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: -2.35 (0.46), residues: 265 helix: -0.96 (0.32), residues: 224 sheet: None (None), residues: 0 loop : -4.12 (0.70), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 600 HIS 0.003 0.001 HIS A 561 PHE 0.013 0.002 PHE A 553 TYR 0.025 0.002 TYR A 488 ARG 0.004 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.287 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2631 time to fit residues: 10.0851 Evaluate side-chains 24 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.0170 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2252 Z= 0.218 Angle : 0.879 14.116 3037 Z= 0.437 Chirality : 0.045 0.179 326 Planarity : 0.004 0.038 388 Dihedral : 6.550 24.817 306 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 27.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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: -2.00 (0.48), residues: 265 helix: -0.70 (0.33), residues: 223 sheet: None (None), residues: 0 loop : -4.03 (0.71), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 600 HIS 0.003 0.001 HIS A 567 PHE 0.013 0.002 PHE A 553 TYR 0.013 0.002 TYR A 448 ARG 0.002 0.000 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.265 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2213 time to fit residues: 8.3375 Evaluate side-chains 26 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.269 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.6719 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2252 Z= 0.238 Angle : 0.893 13.774 3037 Z= 0.451 Chirality : 0.045 0.163 326 Planarity : 0.004 0.036 388 Dihedral : 6.583 24.380 306 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 27.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.48), residues: 265 helix: -0.67 (0.33), residues: 221 sheet: None (None), residues: 0 loop : -4.07 (0.67), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 600 HIS 0.004 0.001 HIS A 561 PHE 0.012 0.002 PHE A 553 TYR 0.035 0.002 TYR A 488 ARG 0.002 0.000 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.260 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1990 time to fit residues: 7.5738 Evaluate side-chains 26 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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: 0.6703 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2252 Z= 0.221 Angle : 0.890 14.896 3037 Z= 0.441 Chirality : 0.046 0.166 326 Planarity : 0.004 0.035 388 Dihedral : 6.445 23.347 306 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: -1.68 (0.49), residues: 265 helix: -0.43 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -4.20 (0.67), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 600 HIS 0.004 0.001 HIS A 561 PHE 0.011 0.002 PHE A 553 TYR 0.027 0.002 TYR A 488 ARG 0.004 0.000 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.244 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2017 time to fit residues: 8.5346 Evaluate side-chains 27 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.6689 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2252 Z= 0.224 Angle : 0.885 14.614 3037 Z= 0.435 Chirality : 0.046 0.167 326 Planarity : 0.004 0.035 388 Dihedral : 6.455 23.328 306 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 27.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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 (0.49), residues: 265 helix: -0.52 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -4.27 (0.68), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 600 HIS 0.003 0.001 HIS A 567 PHE 0.011 0.002 PHE A 553 TYR 0.027 0.002 TYR A 448 ARG 0.003 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.192 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1940 time to fit residues: 7.5421 Evaluate side-chains 27 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.0050 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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: 0.6671 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2252 Z= 0.237 Angle : 0.929 16.335 3037 Z= 0.458 Chirality : 0.046 0.166 326 Planarity : 0.004 0.033 388 Dihedral : 6.436 25.949 306 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 25.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: -1.70 (0.49), residues: 265 helix: -0.43 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -4.32 (0.67), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 600 HIS 0.003 0.001 HIS A 561 PHE 0.010 0.001 PHE A 553 TYR 0.027 0.002 TYR A 488 ARG 0.003 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.244 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2071 time to fit residues: 7.8348 Evaluate side-chains 25 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.258 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.6697 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2252 Z= 0.252 Angle : 0.980 16.749 3037 Z= 0.494 Chirality : 0.048 0.176 326 Planarity : 0.004 0.032 388 Dihedral : 6.520 24.993 306 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 29.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -1.70 (0.49), residues: 265 helix: -0.42 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -4.28 (0.67), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 461 HIS 0.004 0.001 HIS A 567 PHE 0.016 0.002 PHE A 553 TYR 0.025 0.002 TYR A 488 ARG 0.003 0.000 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.263 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2200 time to fit residues: 8.2929 Evaluate side-chains 27 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.6685 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2252 Z= 0.254 Angle : 0.988 16.807 3037 Z= 0.497 Chirality : 0.050 0.221 326 Planarity : 0.004 0.032 388 Dihedral : 6.481 26.387 306 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 28.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -1.63 (0.50), residues: 265 helix: -0.33 (0.34), residues: 217 sheet: None (None), residues: 0 loop : -4.19 (0.71), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 461 HIS 0.003 0.001 HIS A 561 PHE 0.016 0.002 PHE A 553 TYR 0.026 0.002 TYR A 448 ARG 0.003 0.000 ARG A 483 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.270 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2256 time to fit residues: 8.4954 Evaluate side-chains 27 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.064581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.054430 restraints weight = 20267.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.055632 restraints weight = 14985.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.056533 restraints weight = 11679.015| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2252 Z= 0.249 Angle : 0.963 15.623 3037 Z= 0.481 Chirality : 0.047 0.172 326 Planarity : 0.004 0.036 388 Dihedral : 6.477 25.435 306 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.65 (0.50), residues: 265 helix: -0.34 (0.34), residues: 218 sheet: None (None), residues: 0 loop : -4.31 (0.71), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 461 HIS 0.003 0.001 HIS A 561 PHE 0.014 0.002 PHE A 553 TYR 0.026 0.002 TYR A 448 ARG 0.005 0.001 ARG A 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 979.76 seconds wall clock time: 18 minutes 16.46 seconds (1096.46 seconds total)