null Mon 24 Dec 08:00:49 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ich-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ich-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ich-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.8-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 08:00:53 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/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.8-parrot-noncs/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 509 and 0 Target number of residues in the AU: 509 Target solvent content: 0.6258 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.51 Input MTZ file: 2ich-3.8-parrot-noncs.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: 63.275 95.573 121.745 90.000 90.000 90.000 Input sequence file: 2ich-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.70 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: 29.160 3.800 Wilson plot Bfac: 64.14 7662 reflections ( 99.64 % complete ) and 0 restraints for refining 5918 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3185 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3204 (Rfree = 0.000) for 5918 atoms. Found 32 (32 requested) and removed 68 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 5958 seeds are put forward NCS extension: 0 residues added, 5958 seeds are put forward Round 1: 290 peptides, 55 chains. Longest chain 11 peptides. Score 0.341 Round 2: 338 peptides, 49 chains. Longest chain 18 peptides. Score 0.498 Round 3: 358 peptides, 50 chains. Longest chain 20 peptides. Score 0.528 Round 4: 378 peptides, 50 chains. Longest chain 20 peptides. Score 0.563 Round 5: 394 peptides, 51 chains. Longest chain 19 peptides. Score 0.583 Taking the results from Round 5 Chains 56, Residues 343, Estimated correctness of the model 0.0 % 10 chains (79 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10087 restraints for refining 4845 atoms. 8505 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2684 (Rfree = 0.000) for 4845 atoms. Found 22 (26 requested) and removed 51 (13 requested) atoms. Cycle 2: After refmac, R = 0.2559 (Rfree = 0.000) for 4722 atoms. Found 26 (26 requested) and removed 54 (13 requested) atoms. Cycle 3: After refmac, R = 0.2471 (Rfree = 0.000) for 4651 atoms. Found 25 (25 requested) and removed 54 (12 requested) atoms. Cycle 4: After refmac, R = 0.2296 (Rfree = 0.000) for 4590 atoms. Found 23 (25 requested) and removed 46 (12 requested) atoms. Cycle 5: After refmac, R = 0.1942 (Rfree = 0.000) for 4545 atoms. Found 8 (25 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 4618 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4633 seeds are put forward Round 1: 349 peptides, 61 chains. Longest chain 13 peptides. Score 0.415 Round 2: 388 peptides, 55 chains. Longest chain 23 peptides. Score 0.542 Round 3: 371 peptides, 52 chains. Longest chain 18 peptides. Score 0.535 Round 4: 377 peptides, 51 chains. Longest chain 16 peptides. Score 0.554 Round 5: 383 peptides, 51 chains. Longest chain 21 peptides. Score 0.564 Taking the results from Round 5 Chains 54, Residues 332, Estimated correctness of the model 0.0 % 7 chains (60 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10422 restraints for refining 4847 atoms. 8929 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2542 (Rfree = 0.000) for 4847 atoms. Found 26 (26 requested) and removed 48 (13 requested) atoms. Cycle 7: After refmac, R = 0.2368 (Rfree = 0.000) for 4786 atoms. Found 26 (26 requested) and removed 55 (13 requested) atoms. Cycle 8: After refmac, R = 0.2329 (Rfree = 0.000) for 4734 atoms. Found 26 (26 requested) and removed 58 (13 requested) atoms. Cycle 9: After refmac, R = 0.2223 (Rfree = 0.000) for 4682 atoms. Found 25 (25 requested) and removed 33 (12 requested) atoms. Cycle 10: After refmac, R = 0.2216 (Rfree = 0.000) for 4664 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 4807 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4822 seeds are put forward Round 1: 336 peptides, 56 chains. Longest chain 21 peptides. Score 0.433 Round 2: 362 peptides, 49 chains. Longest chain 21 peptides. Score 0.543 Round 3: 400 peptides, 56 chains. Longest chain 22 peptides. Score 0.555 Round 4: 380 peptides, 53 chains. Longest chain 18 peptides. Score 0.543 Round 5: 385 peptides, 52 chains. Longest chain 22 peptides. Score 0.560 Taking the results from Round 5 Chains 52, Residues 333, Estimated correctness of the model 0.0 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10736 restraints for refining 4847 atoms. 9370 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2503 (Rfree = 0.000) for 4847 atoms. Found 26 (26 requested) and removed 61 (13 requested) atoms. Cycle 12: After refmac, R = 0.2344 (Rfree = 0.000) for 4778 atoms. Found 26 (26 requested) and removed 57 (13 requested) atoms. Cycle 13: After refmac, R = 0.2285 (Rfree = 0.000) for 4738 atoms. Found 26 (26 requested) and removed 47 (13 requested) atoms. Cycle 14: After refmac, R = 0.2133 (Rfree = 0.000) for 4709 atoms. Found 25 (25 requested) and removed 36 (12 requested) atoms. Cycle 15: After refmac, R = 0.1828 (Rfree = 0.000) for 4689 atoms. Found 12 (25 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 4786 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4807 seeds are put forward Round 1: 325 peptides, 54 chains. Longest chain 13 peptides. Score 0.428 Round 2: 354 peptides, 49 chains. Longest chain 16 peptides. Score 0.529 Round 3: 369 peptides, 49 chains. Longest chain 16 peptides. Score 0.556 Round 4: 369 peptides, 51 chains. Longest chain 17 peptides. Score 0.540 Round 5: 387 peptides, 56 chains. Longest chain 21 peptides. Score 0.532 Taking the results from Round 3 Chains 50, Residues 320, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10615 restraints for refining 4848 atoms. 9277 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2362 (Rfree = 0.000) for 4848 atoms. Found 26 (26 requested) and removed 36 (13 requested) atoms. Cycle 17: After refmac, R = 0.2326 (Rfree = 0.000) for 4799 atoms. Found 26 (26 requested) and removed 39 (13 requested) atoms. Cycle 18: After refmac, R = 0.2212 (Rfree = 0.000) for 4764 atoms. Found 26 (26 requested) and removed 35 (13 requested) atoms. Cycle 19: After refmac, R = 0.1758 (Rfree = 0.000) for 4734 atoms. Found 10 (26 requested) and removed 29 (13 requested) atoms. Cycle 20: After refmac, R = 0.1710 (Rfree = 0.000) for 4710 atoms. Found 8 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 4797 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4813 seeds are put forward Round 1: 314 peptides, 56 chains. Longest chain 11 peptides. Score 0.386 Round 2: 374 peptides, 59 chains. Longest chain 14 peptides. Score 0.483 Round 3: 362 peptides, 54 chains. Longest chain 17 peptides. Score 0.502 Round 4: 347 peptides, 52 chains. Longest chain 20 peptides. Score 0.490 Round 5: 359 peptides, 55 chains. Longest chain 23 peptides. Score 0.488 Taking the results from Round 3 Chains 56, Residues 308, Estimated correctness of the model 0.0 % 7 chains (46 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10450 restraints for refining 4848 atoms. 9106 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2433 (Rfree = 0.000) for 4848 atoms. Found 26 (26 requested) and removed 42 (13 requested) atoms. Cycle 22: After refmac, R = 0.2249 (Rfree = 0.000) for 4797 atoms. Found 26 (26 requested) and removed 33 (13 requested) atoms. Cycle 23: After refmac, R = 0.1807 (Rfree = 0.000) for 4778 atoms. Found 14 (26 requested) and removed 22 (13 requested) atoms. Cycle 24: After refmac, R = 0.1770 (Rfree = 0.000) for 4759 atoms. Found 9 (26 requested) and removed 25 (13 requested) atoms. Cycle 25: After refmac, R = 0.1897 (Rfree = 0.000) for 4738 atoms. Found 22 (26 requested) and removed 30 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 4793 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4812 seeds are put forward Round 1: 289 peptides, 56 chains. Longest chain 12 peptides. Score 0.329 Round 2: 338 peptides, 54 chains. Longest chain 14 peptides. Score 0.455 Round 3: 351 peptides, 51 chains. Longest chain 21 peptides. Score 0.506 Round 4: 340 peptides, 49 chains. Longest chain 18 peptides. Score 0.502 Round 5: 339 peptides, 47 chains. Longest chain 19 peptides. Score 0.517 Taking the results from Round 5 Chains 50, Residues 292, Estimated correctness of the model 0.0 % 7 chains (56 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10587 restraints for refining 4848 atoms. 9288 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2258 (Rfree = 0.000) for 4848 atoms. Found 17 (26 requested) and removed 35 (13 requested) atoms. Cycle 27: After refmac, R = 0.2082 (Rfree = 0.000) for 4805 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. Cycle 28: After refmac, R = 0.1841 (Rfree = 0.000) for 4780 atoms. Found 18 (26 requested) and removed 17 (13 requested) atoms. Cycle 29: After refmac, R = 0.1822 (Rfree = 0.000) for 4770 atoms. Found 18 (26 requested) and removed 24 (13 requested) atoms. Cycle 30: After refmac, R = 0.1792 (Rfree = 0.000) for 4752 atoms. Found 19 (26 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 4833 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4855 seeds are put forward Round 1: 294 peptides, 56 chains. Longest chain 12 peptides. Score 0.341 Round 2: 332 peptides, 51 chains. Longest chain 18 peptides. Score 0.469 Round 3: 334 peptides, 53 chains. Longest chain 26 peptides. Score 0.455 Round 4: 342 peptides, 49 chains. Longest chain 42 peptides. Score 0.506 Round 5: 339 peptides, 43 chains. Longest chain 23 peptides. Score 0.550 Taking the results from Round 5 Chains 45, Residues 296, Estimated correctness of the model 0.0 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10843 restraints for refining 4848 atoms. 9574 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2221 (Rfree = 0.000) for 4848 atoms. Found 20 (26 requested) and removed 27 (13 requested) atoms. Cycle 32: After refmac, R = 0.2322 (Rfree = 0.000) for 4806 atoms. Found 26 (26 requested) and removed 34 (13 requested) atoms. Cycle 33: After refmac, R = 0.2160 (Rfree = 0.000) for 4777 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. Cycle 34: After refmac, R = 0.1683 (Rfree = 0.000) for 4760 atoms. Found 14 (26 requested) and removed 23 (13 requested) atoms. Cycle 35: After refmac, R = 0.1588 (Rfree = 0.000) for 4741 atoms. Found 9 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 4846 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4862 seeds are put forward Round 1: 265 peptides, 52 chains. Longest chain 10 peptides. Score 0.312 Round 2: 307 peptides, 52 chains. Longest chain 18 peptides. Score 0.408 Round 3: 302 peptides, 51 chains. Longest chain 11 peptides. Score 0.407 Round 4: 316 peptides, 55 chains. Longest chain 12 peptides. Score 0.399 Round 5: 324 peptides, 49 chains. Longest chain 14 peptides. Score 0.471 Taking the results from Round 5 Chains 49, Residues 275, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 11022 restraints for refining 4848 atoms. 9936 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2315 (Rfree = 0.000) for 4848 atoms. Found 26 (26 requested) and removed 42 (13 requested) atoms. Cycle 37: After refmac, R = 0.2291 (Rfree = 0.000) for 4817 atoms. Found 26 (26 requested) and removed 31 (13 requested) atoms. Cycle 38: After refmac, R = 0.2118 (Rfree = 0.000) for 4797 atoms. Found 26 (26 requested) and removed 30 (13 requested) atoms. Cycle 39: After refmac, R = 0.2106 (Rfree = 0.000) for 4777 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 40: After refmac, R = 0.2126 (Rfree = 0.000) for 4762 atoms. Found 26 (26 requested) and removed 36 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 4843 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4859 seeds are put forward Round 1: 226 peptides, 45 chains. Longest chain 11 peptides. Score 0.290 Round 2: 253 peptides, 43 chains. Longest chain 16 peptides. Score 0.375 Round 3: 287 peptides, 46 chains. Longest chain 14 peptides. Score 0.421 Round 4: 277 peptides, 44 chains. Longest chain 15 peptides. Score 0.419 Round 5: 277 peptides, 44 chains. Longest chain 11 peptides. Score 0.419 Taking the results from Round 3 Chains 46, Residues 241, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10947 restraints for refining 4848 atoms. 9951 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2407 (Rfree = 0.000) for 4848 atoms. Found 26 (26 requested) and removed 37 (13 requested) atoms. Cycle 42: After refmac, R = 0.2372 (Rfree = 0.000) for 4826 atoms. Found 26 (26 requested) and removed 36 (13 requested) atoms. Cycle 43: After refmac, R = 0.1855 (Rfree = 0.000) for 4803 atoms. Found 14 (26 requested) and removed 23 (13 requested) atoms. Cycle 44: After refmac, R = 0.2040 (Rfree = 0.000) for 4781 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 45: After refmac, R = 0.1769 (Rfree = 0.000) for 4777 atoms. Found 16 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 4855 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4875 seeds are put forward Round 1: 226 peptides, 46 chains. Longest chain 8 peptides. Score 0.279 Round 2: 252 peptides, 43 chains. Longest chain 11 peptides. Score 0.372 Round 3: 259 peptides, 39 chains. Longest chain 15 peptides. Score 0.428 Round 4: 263 peptides, 40 chains. Longest chain 13 peptides. Score 0.427 Round 5: 280 peptides, 40 chains. Longest chain 17 peptides. Score 0.463 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 240, Estimated correctness of the model 0.0 % 4 chains (13 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2ich-3_warpNtrace.pdb as input Building loops using Loopy2018 40 chains (240 residues) following loop building 4 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7662 reflections ( 99.64 % complete ) and 11256 restraints for refining 4848 atoms. 10314 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2633 (Rfree = 0.000) for 4848 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2601 (Rfree = 0.000) for 4814 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2548 (Rfree = 0.000) for 4782 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2362 (Rfree = 0.000) for 4757 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:50:53 GMT 2018 Job finished. TimeTaking 50.08 Used memory is bytes: 12269512