null Mon 24 Dec 07:59:12 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 2afb-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2afb-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2afb-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-3.2-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/2afb-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-3.2-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 07:59:17 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/2afb-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-3.2-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 521 and 0 Target number of residues in the AU: 521 Target solvent content: 0.6155 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 702 Adjusted target solvent content: 0.48 Input MTZ file: 2afb-3.2-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 5616 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: 97.203 3.200 Wilson plot Bfac: 59.24 12384 reflections ( 99.61 % complete ) and 0 restraints for refining 6261 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3183 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2463 (Rfree = 0.000) for 6261 atoms. Found 23 (56 requested) and removed 49 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 6319 seeds are put forward NCS extension: 0 residues added, 6319 seeds are put forward Round 1: 326 peptides, 60 chains. Longest chain 16 peptides. Score 0.375 Round 2: 415 peptides, 52 chains. Longest chain 19 peptides. Score 0.611 Round 3: 443 peptides, 51 chains. Longest chain 25 peptides. Score 0.660 Round 4: 473 peptides, 47 chains. Longest chain 37 peptides. Score 0.723 Round 5: 485 peptides, 44 chains. Longest chain 42 peptides. Score 0.752 Taking the results from Round 5 Chains 49, Residues 441, Estimated correctness of the model 75.4 % 10 chains (147 residues) have been docked in sequence Building loops using Loopy2018 49 chains (441 residues) following loop building 10 chains (147 residues) in sequence following loop building ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 9546 restraints for refining 5123 atoms. 7305 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2885 (Rfree = 0.000) for 5123 atoms. Found 34 (46 requested) and removed 79 (23 requested) atoms. Cycle 2: After refmac, R = 0.2760 (Rfree = 0.000) for 4993 atoms. Found 31 (44 requested) and removed 39 (22 requested) atoms. Cycle 3: After refmac, R = 0.2732 (Rfree = 0.000) for 4937 atoms. Found 29 (42 requested) and removed 32 (22 requested) atoms. Cycle 4: After refmac, R = 0.2488 (Rfree = 0.000) for 4908 atoms. Found 18 (41 requested) and removed 28 (22 requested) atoms. Cycle 5: After refmac, R = 0.2579 (Rfree = 0.000) for 4882 atoms. Found 16 (40 requested) and removed 34 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 5089 seeds are put forward NCS extension: 27 residues added (29 deleted due to clashes), 5116 seeds are put forward Round 1: 420 peptides, 49 chains. Longest chain 35 peptides. Score 0.640 Round 2: 442 peptides, 42 chains. Longest chain 36 peptides. Score 0.714 Round 3: 435 peptides, 42 chains. Longest chain 36 peptides. Score 0.705 Round 4: 452 peptides, 51 chains. Longest chain 44 peptides. Score 0.672 Round 5: 459 peptides, 47 chains. Longest chain 28 peptides. Score 0.706 Taking the results from Round 2 Chains 48, Residues 400, Estimated correctness of the model 68.1 % 9 chains (150 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 127 A and 134 A 46 chains (401 residues) following loop building 8 chains (156 residues) in sequence following loop building ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 9894 restraints for refining 5127 atoms. 7737 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2947 (Rfree = 0.000) for 5127 atoms. Found 37 (41 requested) and removed 69 (23 requested) atoms. Cycle 7: After refmac, R = 0.2722 (Rfree = 0.000) for 5058 atoms. Found 24 (40 requested) and removed 35 (22 requested) atoms. Cycle 8: After refmac, R = 0.2625 (Rfree = 0.000) for 5012 atoms. Found 18 (39 requested) and removed 28 (22 requested) atoms. Cycle 9: After refmac, R = 0.2574 (Rfree = 0.000) for 4981 atoms. Found 14 (37 requested) and removed 26 (22 requested) atoms. Cycle 10: After refmac, R = 0.2573 (Rfree = 0.000) for 4954 atoms. Found 19 (36 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 5148 seeds are put forward NCS extension: 55 residues added (27 deleted due to clashes), 5203 seeds are put forward Round 1: 395 peptides, 49 chains. Longest chain 26 peptides. Score 0.601 Round 2: 440 peptides, 51 chains. Longest chain 28 peptides. Score 0.656 Round 3: 445 peptides, 47 chains. Longest chain 28 peptides. Score 0.688 Round 4: 426 peptides, 43 chains. Longest chain 33 peptides. Score 0.687 Round 5: 430 peptides, 50 chains. Longest chain 25 peptides. Score 0.648 Taking the results from Round 3 Chains 49, Residues 398, Estimated correctness of the model 62.6 % 8 chains (114 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 10411 restraints for refining 5126 atoms. 8424 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2819 (Rfree = 0.000) for 5126 atoms. Found 37 (37 requested) and removed 39 (23 requested) atoms. Cycle 12: After refmac, R = 0.2785 (Rfree = 0.000) for 5086 atoms. Found 36 (36 requested) and removed 36 (22 requested) atoms. Cycle 13: After refmac, R = 0.2678 (Rfree = 0.000) for 5064 atoms. Found 26 (36 requested) and removed 32 (22 requested) atoms. Cycle 14: After refmac, R = 0.2674 (Rfree = 0.000) for 5032 atoms. Found 31 (36 requested) and removed 32 (22 requested) atoms. Cycle 15: After refmac, R = 0.2469 (Rfree = 0.000) for 5011 atoms. Found 11 (36 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.33 Search for helices and strands: 0 residues in 0 chains, 5173 seeds are put forward NCS extension: 25 residues added (15 deleted due to clashes), 5198 seeds are put forward Round 1: 410 peptides, 57 chains. Longest chain 22 peptides. Score 0.566 Round 2: 425 peptides, 45 chains. Longest chain 34 peptides. Score 0.673 Round 3: 448 peptides, 54 chains. Longest chain 23 peptides. Score 0.647 Round 4: 441 peptides, 51 chains. Longest chain 23 peptides. Score 0.657 Round 5: 440 peptides, 47 chains. Longest chain 34 peptides. Score 0.681 Taking the results from Round 5 Chains 50, Residues 393, Estimated correctness of the model 61.0 % 4 chains (91 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 10273 restraints for refining 5127 atoms. 8359 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2753 (Rfree = 0.000) for 5127 atoms. Found 26 (37 requested) and removed 45 (23 requested) atoms. Cycle 17: After refmac, R = 0.2696 (Rfree = 0.000) for 5073 atoms. Found 33 (36 requested) and removed 30 (22 requested) atoms. Cycle 18: After refmac, R = 0.2615 (Rfree = 0.000) for 5049 atoms. Found 33 (36 requested) and removed 28 (22 requested) atoms. Cycle 19: After refmac, R = 0.2543 (Rfree = 0.000) for 5039 atoms. Found 24 (36 requested) and removed 33 (22 requested) atoms. Cycle 20: After refmac, R = 0.2481 (Rfree = 0.000) for 5020 atoms. Found 19 (36 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 5195 seeds are put forward NCS extension: 49 residues added (12 deleted due to clashes), 5244 seeds are put forward Round 1: 427 peptides, 59 chains. Longest chain 25 peptides. Score 0.580 Round 2: 453 peptides, 53 chains. Longest chain 34 peptides. Score 0.661 Round 3: 451 peptides, 54 chains. Longest chain 26 peptides. Score 0.652 Round 4: 444 peptides, 47 chains. Longest chain 35 peptides. Score 0.686 Round 5: 451 peptides, 53 chains. Longest chain 27 peptides. Score 0.658 Taking the results from Round 4 Chains 51, Residues 397, Estimated correctness of the model 62.2 % 5 chains (108 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 9999 restraints for refining 5126 atoms. 7999 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2777 (Rfree = 0.000) for 5126 atoms. Found 24 (37 requested) and removed 45 (23 requested) atoms. Cycle 22: After refmac, R = 0.2628 (Rfree = 0.000) for 5084 atoms. Found 26 (36 requested) and removed 29 (22 requested) atoms. Cycle 23: After refmac, R = 0.2336 (Rfree = 0.000) for 5065 atoms. Found 10 (36 requested) and removed 26 (22 requested) atoms. Cycle 24: After refmac, R = 0.2513 (Rfree = 0.000) for 5040 atoms. Found 26 (36 requested) and removed 26 (22 requested) atoms. Cycle 25: After refmac, R = 0.2191 (Rfree = 0.000) for 5021 atoms. Found 11 (36 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 3.19 Search for helices and strands: 0 residues in 0 chains, 5167 seeds are put forward NCS extension: 31 residues added (11 deleted due to clashes), 5198 seeds are put forward Round 1: 379 peptides, 52 chains. Longest chain 23 peptides. Score 0.551 Round 2: 441 peptides, 51 chains. Longest chain 26 peptides. Score 0.657 Round 3: 431 peptides, 47 chains. Longest chain 25 peptides. Score 0.669 Round 4: 420 peptides, 44 chains. Longest chain 34 peptides. Score 0.673 Round 5: 431 peptides, 49 chains. Longest chain 23 peptides. Score 0.656 Taking the results from Round 4 Chains 45, Residues 376, Estimated correctness of the model 59.2 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 10914 restraints for refining 5127 atoms. 9285 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2471 (Rfree = 0.000) for 5127 atoms. Found 34 (37 requested) and removed 37 (23 requested) atoms. Cycle 27: After refmac, R = 0.2357 (Rfree = 0.000) for 5111 atoms. Found 24 (36 requested) and removed 25 (22 requested) atoms. Cycle 28: After refmac, R = 0.2316 (Rfree = 0.000) for 5102 atoms. Found 19 (36 requested) and removed 26 (22 requested) atoms. Cycle 29: After refmac, R = 0.2263 (Rfree = 0.000) for 5091 atoms. Found 15 (36 requested) and removed 24 (22 requested) atoms. Cycle 30: After refmac, R = 0.2238 (Rfree = 0.000) for 5074 atoms. Found 23 (36 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 5234 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 5250 seeds are put forward Round 1: 371 peptides, 55 chains. Longest chain 18 peptides. Score 0.512 Round 2: 405 peptides, 53 chains. Longest chain 28 peptides. Score 0.588 Round 3: 400 peptides, 47 chains. Longest chain 31 peptides. Score 0.623 Round 4: 406 peptides, 51 chains. Longest chain 35 peptides. Score 0.604 Round 5: 397 peptides, 49 chains. Longest chain 28 peptides. Score 0.604 Taking the results from Round 3 Chains 47, Residues 353, Estimated correctness of the model 47.1 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 11448 restraints for refining 5127 atoms. 10056 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2299 (Rfree = 0.000) for 5127 atoms. Found 14 (37 requested) and removed 26 (23 requested) atoms. Cycle 32: After refmac, R = 0.2242 (Rfree = 0.000) for 5104 atoms. Found 19 (36 requested) and removed 26 (22 requested) atoms. Cycle 33: After refmac, R = 0.2240 (Rfree = 0.000) for 5090 atoms. Found 17 (36 requested) and removed 23 (22 requested) atoms. Cycle 34: After refmac, R = 0.2192 (Rfree = 0.000) for 5078 atoms. Found 13 (36 requested) and removed 23 (22 requested) atoms. Cycle 35: After refmac, R = 0.2142 (Rfree = 0.000) for 5066 atoms. Found 9 (36 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 3.22 Search for helices and strands: 0 residues in 0 chains, 5221 seeds are put forward NCS extension: 18 residues added (13 deleted due to clashes), 5239 seeds are put forward Round 1: 356 peptides, 57 chains. Longest chain 18 peptides. Score 0.466 Round 2: 404 peptides, 49 chains. Longest chain 34 peptides. Score 0.615 Round 3: 403 peptides, 50 chains. Longest chain 19 peptides. Score 0.606 Round 4: 420 peptides, 50 chains. Longest chain 31 peptides. Score 0.633 Round 5: 415 peptides, 56 chains. Longest chain 19 peptides. Score 0.582 Taking the results from Round 4 Chains 54, Residues 370, Estimated correctness of the model 49.7 % 5 chains (73 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 10582 restraints for refining 5125 atoms. 8855 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2339 (Rfree = 0.000) for 5125 atoms. Found 22 (37 requested) and removed 30 (23 requested) atoms. Cycle 37: After refmac, R = 0.2296 (Rfree = 0.000) for 5098 atoms. Found 14 (36 requested) and removed 23 (22 requested) atoms. Cycle 38: After refmac, R = 0.2324 (Rfree = 0.000) for 5079 atoms. Found 18 (36 requested) and removed 24 (22 requested) atoms. Cycle 39: After refmac, R = 0.2288 (Rfree = 0.000) for 5065 atoms. Found 14 (36 requested) and removed 23 (22 requested) atoms. Cycle 40: After refmac, R = 0.2294 (Rfree = 0.000) for 5047 atoms. Found 11 (36 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 5191 seeds are put forward NCS extension: 17 residues added (12 deleted due to clashes), 5208 seeds are put forward Round 1: 362 peptides, 54 chains. Longest chain 18 peptides. Score 0.503 Round 2: 400 peptides, 50 chains. Longest chain 27 peptides. Score 0.602 Round 3: 414 peptides, 47 chains. Longest chain 27 peptides. Score 0.644 Round 4: 404 peptides, 50 chains. Longest chain 30 peptides. Score 0.608 Round 5: 396 peptides, 45 chains. Longest chain 31 peptides. Score 0.631 Taking the results from Round 3 Chains 54, Residues 367, Estimated correctness of the model 52.4 % 5 chains (57 residues) have been docked in sequence ------------------------------------------------------ 12384 reflections ( 99.61 % complete ) and 10739 restraints for refining 5127 atoms. 9100 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2345 (Rfree = 0.000) for 5127 atoms. Found 15 (37 requested) and removed 28 (23 requested) atoms. Cycle 42: After refmac, R = 0.2337 (Rfree = 0.000) for 5103 atoms. Found 20 (36 requested) and removed 24 (22 requested) atoms. Cycle 43: After refmac, R = 0.2265 (Rfree = 0.000) for 5088 atoms. Found 26 (36 requested) and removed 26 (22 requested) atoms. Cycle 44: After refmac, R = 0.2249 (Rfree = 0.000) for 5077 atoms. Found 16 (36 requested) and removed 25 (22 requested) atoms. Cycle 45: After refmac, R = 0.2205 (Rfree = 0.000) for 5060 atoms. Found 23 (36 requested) and removed 30 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 5200 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 5230 seeds are put forward Round 1: 354 peptides, 54 chains. Longest chain 20 peptides. Score 0.488 Round 2: 385 peptides, 49 chains. Longest chain 27 peptides. Score 0.584 Round 3: 396 peptides, 56 chains. Longest chain 22 peptides. Score 0.549 Round 4: 386 peptides, 49 chains. Longest chain 27 peptides. Score 0.586 Round 5: 404 peptides, 54 chains. Longest chain 23 peptides. Score 0.579 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 337, Estimated correctness of the model 37.2 % 7 chains (64 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2afb-3_warpNtrace.pdb as input Building loops using Loopy2018 51 chains (337 residues) following loop building 7 chains (64 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12384 reflections ( 99.61 % complete ) and 10841 restraints for refining 5127 atoms. 9310 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2418 (Rfree = 0.000) for 5127 atoms. Found 0 (37 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.2439 (Rfree = 0.000) for 5091 atoms. Found 0 (36 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.2343 (Rfree = 0.000) for 5065 atoms. Found 0 (36 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.2121 (Rfree = 0.000) for 5036 atoms. Found 0 (36 requested) and removed 22 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:05:47 GMT 2018 Job finished. TimeTaking 66.59 Used memory is bytes: 23888088