Sun 23 Dec 22:22:53 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hx1-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hx1-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hx1-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:03 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-4.0-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 800 and 0 Target number of residues in the AU: 800 Target solvent content: 0.6349 Checking the provided sequence file Detected sequence length: 284 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1136 Adjusted target solvent content: 0.48 Input MTZ file: 2hx1-4.0-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 9088 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 93.753 4.000 Wilson plot Bfac: 69.10 10515 reflections ( 99.59 % complete ) and 0 restraints for refining 10034 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3420 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3418 (Rfree = 0.000) for 10034 atoms. Found 47 (47 requested) and removed 49 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 10240 seeds are put forward NCS extension: 0 residues added, 10240 seeds are put forward Round 1: 353 peptides, 76 chains. Longest chain 9 peptides. Score 0.249 Round 2: 462 peptides, 84 chains. Longest chain 12 peptides. Score 0.362 Round 3: 546 peptides, 89 chains. Longest chain 19 peptides. Score 0.446 Round 4: 593 peptides, 91 chains. Longest chain 20 peptides. Score 0.493 Round 5: 585 peptides, 84 chains. Longest chain 24 peptides. Score 0.520 Taking the results from Round 5 Chains 84, Residues 501, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19346 restraints for refining 8206 atoms. 17426 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3371 (Rfree = 0.000) for 8206 atoms. Found 38 (38 requested) and removed 49 (19 requested) atoms. Cycle 2: After refmac, R = 0.3456 (Rfree = 0.000) for 8001 atoms. Found 38 (38 requested) and removed 54 (19 requested) atoms. Cycle 3: After refmac, R = 0.3147 (Rfree = 0.000) for 7876 atoms. Found 37 (37 requested) and removed 41 (18 requested) atoms. Cycle 4: After refmac, R = 0.2941 (Rfree = 0.000) for 7802 atoms. Found 32 (37 requested) and removed 40 (18 requested) atoms. Cycle 5: After refmac, R = 0.2295 (Rfree = 0.000) for 7748 atoms. Found 20 (37 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 8024 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 8045 seeds are put forward Round 1: 449 peptides, 92 chains. Longest chain 15 peptides. Score 0.294 Round 2: 536 peptides, 87 chains. Longest chain 21 peptides. Score 0.444 Round 3: 570 peptides, 85 chains. Longest chain 20 peptides. Score 0.497 Round 4: 603 peptides, 87 chains. Longest chain 18 peptides. Score 0.525 Round 5: 609 peptides, 81 chains. Longest chain 23 peptides. Score 0.561 Taking the results from Round 5 Chains 83, Residues 528, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 18370 restraints for refining 8052 atoms. 16313 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2588 (Rfree = 0.000) for 8052 atoms. Found 38 (38 requested) and removed 57 (19 requested) atoms. Cycle 7: After refmac, R = 0.2594 (Rfree = 0.000) for 7923 atoms. Found 38 (38 requested) and removed 52 (19 requested) atoms. Cycle 8: After refmac, R = 0.2129 (Rfree = 0.000) for 7838 atoms. Found 17 (37 requested) and removed 30 (18 requested) atoms. Cycle 9: After refmac, R = 0.2075 (Rfree = 0.000) for 7775 atoms. Found 18 (37 requested) and removed 32 (18 requested) atoms. Cycle 10: After refmac, R = 0.1873 (Rfree = 0.000) for 7737 atoms. Found 7 (36 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 7964 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7977 seeds are put forward Round 1: 487 peptides, 93 chains. Longest chain 17 peptides. Score 0.343 Round 2: 557 peptides, 84 chains. Longest chain 21 peptides. Score 0.487 Round 3: 592 peptides, 86 chains. Longest chain 17 peptides. Score 0.518 Round 4: 614 peptides, 84 chains. Longest chain 18 peptides. Score 0.552 Round 5: 610 peptides, 80 chains. Longest chain 20 peptides. Score 0.567 Taking the results from Round 5 Chains 81, Residues 530, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 18541 restraints for refining 8156 atoms. 16473 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3142 (Rfree = 0.000) for 8156 atoms. Found 38 (38 requested) and removed 84 (19 requested) atoms. Cycle 12: After refmac, R = 0.2918 (Rfree = 0.000) for 8042 atoms. Found 38 (38 requested) and removed 299 (19 requested) atoms. Cycle 13: After refmac, R = 0.2927 (Rfree = 0.000) for 7739 atoms. Found 36 (36 requested) and removed 67 (18 requested) atoms. Cycle 14: After refmac, R = 0.2802 (Rfree = 0.000) for 7673 atoms. Found 36 (36 requested) and removed 67 (18 requested) atoms. Cycle 15: After refmac, R = 0.2373 (Rfree = 0.000) for 7629 atoms. Found 12 (36 requested) and removed 136 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 7632 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 7656 seeds are put forward Round 1: 406 peptides, 84 chains. Longest chain 9 peptides. Score 0.280 Round 2: 455 peptides, 79 chains. Longest chain 14 peptides. Score 0.382 Round 3: 469 peptides, 84 chains. Longest chain 11 peptides. Score 0.372 Round 4: 517 peptides, 78 chains. Longest chain 15 peptides. Score 0.470 Round 5: 521 peptides, 86 chains. Longest chain 11 peptides. Score 0.430 Taking the results from Round 4 Chains 79, Residues 439, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19142 restraints for refining 8208 atoms. 17424 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3143 (Rfree = 0.000) for 8208 atoms. Found 38 (38 requested) and removed 118 (19 requested) atoms. Cycle 17: After refmac, R = 0.2994 (Rfree = 0.000) for 8057 atoms. Found 38 (38 requested) and removed 68 (19 requested) atoms. Cycle 18: After refmac, R = 0.2730 (Rfree = 0.000) for 7987 atoms. Found 38 (38 requested) and removed 63 (19 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2254 (Rfree = 0.000) for 7923 atoms. Found 28 (37 requested) and removed 45 (18 requested) atoms. Cycle 20: After refmac, R = 0.2160 (Rfree = 0.000) for 7880 atoms. Found 30 (37 requested) and removed 45 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 8088 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 8106 seeds are put forward Round 1: 433 peptides, 90 chains. Longest chain 9 peptides. Score 0.283 Round 2: 507 peptides, 85 chains. Longest chain 14 peptides. Score 0.417 Round 3: 528 peptides, 80 chains. Longest chain 19 peptides. Score 0.472 Round 4: 553 peptides, 86 chains. Longest chain 18 peptides. Score 0.471 Round 5: 526 peptides, 79 chains. Longest chain 20 peptides. Score 0.475 Taking the results from Round 5 Chains 79, Residues 447, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19389 restraints for refining 8208 atoms. 17680 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3050 (Rfree = 0.000) for 8208 atoms. Found 38 (38 requested) and removed 68 (19 requested) atoms. Cycle 22: After refmac, R = 0.2206 (Rfree = 0.000) for 8114 atoms. Found 26 (38 requested) and removed 51 (19 requested) atoms. Cycle 23: After refmac, R = 0.2517 (Rfree = 0.000) for 8054 atoms. Found 38 (38 requested) and removed 50 (19 requested) atoms. Cycle 24: After refmac, R = 0.2457 (Rfree = 0.000) for 8010 atoms. Found 38 (38 requested) and removed 53 (19 requested) atoms. Cycle 25: After refmac, R = 0.1929 (Rfree = 0.000) for 7972 atoms. Found 18 (37 requested) and removed 38 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 8135 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 8170 seeds are put forward Round 1: 420 peptides, 88 chains. Longest chain 12 peptides. Score 0.275 Round 2: 478 peptides, 88 chains. Longest chain 12 peptides. Score 0.360 Round 3: 481 peptides, 82 chains. Longest chain 13 peptides. Score 0.400 Round 4: 499 peptides, 82 chains. Longest chain 18 peptides. Score 0.424 Round 5: 515 peptides, 79 chains. Longest chain 14 peptides. Score 0.462 Taking the results from Round 5 Chains 79, Residues 436, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19206 restraints for refining 8208 atoms. 17541 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2863 (Rfree = 0.000) for 8208 atoms. Found 38 (38 requested) and removed 52 (19 requested) atoms. Cycle 27: After refmac, R = 0.2621 (Rfree = 0.000) for 8114 atoms. Found 38 (38 requested) and removed 59 (19 requested) atoms. Cycle 28: After refmac, R = 0.2442 (Rfree = 0.000) for 8051 atoms. Found 38 (38 requested) and removed 46 (19 requested) atoms. Cycle 29: After refmac, R = 0.2120 (Rfree = 0.000) for 8017 atoms. Found 37 (38 requested) and removed 32 (19 requested) atoms. Cycle 30: After refmac, R = 0.2073 (Rfree = 0.000) for 8003 atoms. Found 10 (38 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 8132 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 8144 seeds are put forward Round 1: 420 peptides, 85 chains. Longest chain 11 peptides. Score 0.294 Round 2: 456 peptides, 83 chains. Longest chain 12 peptides. Score 0.359 Round 3: 490 peptides, 85 chains. Longest chain 12 peptides. Score 0.395 Round 4: 482 peptides, 81 chains. Longest chain 13 peptides. Score 0.407 Round 5: 493 peptides, 83 chains. Longest chain 12 peptides. Score 0.410 Taking the results from Round 5 Chains 83, Residues 410, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19213 restraints for refining 8206 atoms. 17656 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2928 (Rfree = 0.000) for 8206 atoms. Found 38 (38 requested) and removed 79 (19 requested) atoms. Cycle 32: After refmac, R = 0.2581 (Rfree = 0.000) for 8105 atoms. Found 38 (38 requested) and removed 50 (19 requested) atoms. Cycle 33: After refmac, R = 0.2216 (Rfree = 0.000) for 8052 atoms. Found 34 (38 requested) and removed 37 (19 requested) atoms. Cycle 34: After refmac, R = 0.2244 (Rfree = 0.000) for 8029 atoms. Found 19 (38 requested) and removed 36 (19 requested) atoms. Cycle 35: After refmac, R = 0.2149 (Rfree = 0.000) for 7997 atoms. Found 28 (38 requested) and removed 44 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 8179 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 8192 seeds are put forward Round 1: 384 peptides, 82 chains. Longest chain 10 peptides. Score 0.258 Round 2: 444 peptides, 84 chains. Longest chain 12 peptides. Score 0.336 Round 3: 436 peptides, 78 chains. Longest chain 13 peptides. Score 0.361 Round 4: 441 peptides, 79 chains. Longest chain 14 peptides. Score 0.362 Round 5: 436 peptides, 79 chains. Longest chain 11 peptides. Score 0.355 Taking the results from Round 4 Chains 80, Residues 362, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19354 restraints for refining 8207 atoms. 17947 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2807 (Rfree = 0.000) for 8207 atoms. Found 38 (38 requested) and removed 53 (19 requested) atoms. Cycle 37: After refmac, R = 0.2562 (Rfree = 0.000) for 8117 atoms. Found 38 (38 requested) and removed 37 (19 requested) atoms. Cycle 38: After refmac, R = 0.2521 (Rfree = 0.000) for 8064 atoms. Found 38 (38 requested) and removed 42 (19 requested) atoms. Cycle 39: After refmac, R = 0.1932 (Rfree = 0.000) for 8015 atoms. Found 26 (38 requested) and removed 29 (19 requested) atoms. Cycle 40: After refmac, R = 0.1641 (Rfree = 0.000) for 7982 atoms. Found 23 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 8139 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 8153 seeds are put forward Round 1: 324 peptides, 75 chains. Longest chain 7 peptides. Score 0.208 Round 2: 399 peptides, 79 chains. Longest chain 14 peptides. Score 0.301 Round 3: 392 peptides, 75 chains. Longest chain 12 peptides. Score 0.316 Round 4: 390 peptides, 72 chains. Longest chain 13 peptides. Score 0.332 Round 5: 377 peptides, 73 chains. Longest chain 10 peptides. Score 0.306 Taking the results from Round 4 Chains 72, Residues 318, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10515 reflections ( 99.59 % complete ) and 19229 restraints for refining 8058 atoms. 18029 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2629 (Rfree = 0.000) for 8058 atoms. Found 38 (38 requested) and removed 57 (19 requested) atoms. Cycle 42: After refmac, R = 0.2345 (Rfree = 0.000) for 7994 atoms. Found 38 (38 requested) and removed 49 (19 requested) atoms. Cycle 43: After refmac, R = 0.2438 (Rfree = 0.000) for 7954 atoms. Found 37 (37 requested) and removed 51 (18 requested) atoms. Cycle 44: After refmac, R = 0.2492 (Rfree = 0.000) for 7896 atoms. Found 37 (37 requested) and removed 54 (18 requested) atoms. Cycle 45: After refmac, R = 0.2302 (Rfree = 0.000) for 7852 atoms. Found 37 (37 requested) and removed 37 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 7994 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 8015 seeds are put forward Round 1: 310 peptides, 71 chains. Longest chain 7 peptides. Score 0.212 Round 2: 332 peptides, 63 chains. Longest chain 15 peptides. Score 0.303 Round 3: 335 peptides, 62 chains. Longest chain 15 peptides. Score 0.314 Round 4: 344 peptides, 65 chains. Longest chain 9 peptides. Score 0.308 Round 5: 366 peptides, 65 chains. Longest chain 14 peptides. Score 0.342 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 65, Residues 301, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 2hx1-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10515 reflections ( 99.59 % complete ) and 18302 restraints for refining 7789 atoms. 17142 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2502 (Rfree = 0.000) for 7789 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2229 (Rfree = 0.000) for 7744 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2384 (Rfree = 0.000) for 7690 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2056 (Rfree = 0.000) for 7662 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Writing output files ... TimeTaking 90.73