null Sun 23 Dec 23:47:52 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2avn-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2avn-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2avn-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-3.2-parrot-mrncs ############### 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 23:47:56 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/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-3.2-parrot-mrncs/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 678 and 0 Target number of residues in the AU: 678 Target solvent content: 0.6234 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 520 Adjusted target solvent content: 0.71 Input MTZ file: 2avn-3.2-parrot-mrncs.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: 181 Cell parameters: 133.767 133.767 188.622 90.000 90.000 120.000 Input sequence file: 2avn-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4160 target number of atoms Had to go as low as 1.15 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: 115.845 3.200 Wilson plot Bfac: 63.12 17047 reflections ( 99.73 % complete ) and 0 restraints for refining 4628 atoms. Observations/parameters ratio is 0.92 ------------------------------------------------------ Starting model: R = 0.3481 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3421 (Rfree = 0.000) for 4628 atoms. Found 41 (41 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 2.43 Search for helices and strands: 0 residues in 0 chains, 4732 seeds are put forward NCS extension: 0 residues added, 4732 seeds are put forward Round 1: 358 peptides, 46 chains. Longest chain 23 peptides. Score 0.492 Round 2: 403 peptides, 41 chains. Longest chain 24 peptides. Score 0.588 Round 3: 404 peptides, 35 chains. Longest chain 51 peptides. Score 0.625 Round 4: 396 peptides, 37 chains. Longest chain 31 peptides. Score 0.603 Round 5: 384 peptides, 36 chains. Longest chain 25 peptides. Score 0.594 Taking the results from Round 3 Chains 37, Residues 369, Estimated correctness of the model 47.6 % 4 chains (92 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 7290 restraints for refining 3997 atoms. 5473 conditional restraints added. Observations/parameters ratio is 1.07 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3012 (Rfree = 0.000) for 3997 atoms. Found 35 (35 requested) and removed 35 (17 requested) atoms. Cycle 2: After refmac, R = 0.2810 (Rfree = 0.000) for 3929 atoms. Found 35 (35 requested) and removed 25 (17 requested) atoms. Cycle 3: After refmac, R = 0.2671 (Rfree = 0.000) for 3904 atoms. Found 30 (35 requested) and removed 19 (17 requested) atoms. Cycle 4: After refmac, R = 0.2590 (Rfree = 0.000) for 3897 atoms. Found 18 (35 requested) and removed 19 (17 requested) atoms. Cycle 5: After refmac, R = 0.2532 (Rfree = 0.000) for 3885 atoms. Found 19 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 2.37 Search for helices and strands: 0 residues in 0 chains, 4040 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 4069 seeds are put forward Round 1: 400 peptides, 39 chains. Longest chain 27 peptides. Score 0.596 Round 2: 408 peptides, 35 chains. Longest chain 42 peptides. Score 0.630 Round 3: 411 peptides, 35 chains. Longest chain 32 peptides. Score 0.634 Round 4: 400 peptides, 32 chains. Longest chain 30 peptides. Score 0.638 Round 5: 416 peptides, 35 chains. Longest chain 31 peptides. Score 0.640 Taking the results from Round 5 Chains 38, Residues 381, Estimated correctness of the model 51.4 % 6 chains (110 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 7392 restraints for refining 4042 atoms. 5411 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2873 (Rfree = 0.000) for 4042 atoms. Found 36 (36 requested) and removed 25 (18 requested) atoms. Cycle 7: After refmac, R = 0.2717 (Rfree = 0.000) for 4025 atoms. Found 36 (36 requested) and removed 21 (18 requested) atoms. Cycle 8: After refmac, R = 0.2774 (Rfree = 0.000) for 4020 atoms. Found 36 (36 requested) and removed 24 (18 requested) atoms. Cycle 9: After refmac, R = 0.2769 (Rfree = 0.000) for 4018 atoms. Found 36 (36 requested) and removed 23 (18 requested) atoms. Cycle 10: After refmac, R = 0.2575 (Rfree = 0.000) for 4015 atoms. Found 36 (36 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 2.35 Search for helices and strands: 0 residues in 0 chains, 4158 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 4191 seeds are put forward Round 1: 402 peptides, 35 chains. Longest chain 29 peptides. Score 0.623 Round 2: 411 peptides, 37 chains. Longest chain 26 peptides. Score 0.622 Round 3: 426 peptides, 37 chains. Longest chain 31 peptides. Score 0.640 Round 4: 417 peptides, 35 chains. Longest chain 32 peptides. Score 0.641 Round 5: 426 peptides, 33 chains. Longest chain 27 peptides. Score 0.662 Taking the results from Round 5 Chains 37, Residues 393, Estimated correctness of the model 56.7 % 6 chains (93 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 7421 restraints for refining 4028 atoms. 5470 conditional restraints added. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2853 (Rfree = 0.000) for 4028 atoms. Found 36 (36 requested) and removed 33 (18 requested) atoms. Cycle 12: After refmac, R = 0.2701 (Rfree = 0.000) for 4008 atoms. Found 36 (36 requested) and removed 20 (18 requested) atoms. Cycle 13: After refmac, R = 0.2752 (Rfree = 0.000) for 4010 atoms. Found 36 (36 requested) and removed 27 (18 requested) atoms. Cycle 14: After refmac, R = 0.2599 (Rfree = 0.000) for 4010 atoms. Found 33 (36 requested) and removed 19 (18 requested) atoms. Cycle 15: After refmac, R = 0.2638 (Rfree = 0.000) for 4016 atoms. Found 28 (36 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 2.38 Search for helices and strands: 0 residues in 0 chains, 4152 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 4169 seeds are put forward Round 1: 398 peptides, 37 chains. Longest chain 27 peptides. Score 0.606 Round 2: 437 peptides, 32 chains. Longest chain 43 peptides. Score 0.680 Round 3: 425 peptides, 35 chains. Longest chain 36 peptides. Score 0.650 Round 4: 445 peptides, 35 chains. Longest chain 48 peptides. Score 0.672 Round 5: 440 peptides, 32 chains. Longest chain 45 peptides. Score 0.683 Taking the results from Round 5 Chains 36, Residues 408, Estimated correctness of the model 61.5 % 8 chains (189 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6571 restraints for refining 4066 atoms. 4171 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2785 (Rfree = 0.000) for 4066 atoms. Found 36 (36 requested) and removed 31 (18 requested) atoms. Cycle 17: After refmac, R = 0.2551 (Rfree = 0.000) for 4053 atoms. Found 24 (36 requested) and removed 20 (18 requested) atoms. Cycle 18: After refmac, R = 0.2463 (Rfree = 0.000) for 4037 atoms. Found 22 (36 requested) and removed 20 (18 requested) atoms. Cycle 19: After refmac, R = 0.2411 (Rfree = 0.000) for 4018 atoms. Found 22 (36 requested) and removed 18 (18 requested) atoms. Cycle 20: After refmac, R = 0.2489 (Rfree = 0.000) for 4010 atoms. Found 36 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 2.40 Search for helices and strands: 0 residues in 0 chains, 4162 seeds are put forward NCS extension: 13 residues added (41 deleted due to clashes), 4175 seeds are put forward Round 1: 414 peptides, 35 chains. Longest chain 46 peptides. Score 0.637 Round 2: 429 peptides, 32 chains. Longest chain 32 peptides. Score 0.671 Round 3: 419 peptides, 32 chains. Longest chain 36 peptides. Score 0.660 Round 4: 433 peptides, 30 chains. Longest chain 50 peptides. Score 0.686 Round 5: 419 peptides, 35 chains. Longest chain 42 peptides. Score 0.643 Taking the results from Round 4 Chains 36, Residues 403, Estimated correctness of the model 62.2 % 7 chains (172 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6943 restraints for refining 4127 atoms. 4594 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2937 (Rfree = 0.000) for 4127 atoms. Found 37 (37 requested) and removed 40 (18 requested) atoms. Cycle 22: After refmac, R = 0.2652 (Rfree = 0.000) for 4102 atoms. Found 34 (37 requested) and removed 25 (18 requested) atoms. Cycle 23: After refmac, R = 0.2494 (Rfree = 0.000) for 4093 atoms. Found 25 (36 requested) and removed 20 (18 requested) atoms. Cycle 24: After refmac, R = 0.2390 (Rfree = 0.000) for 4085 atoms. Found 16 (36 requested) and removed 20 (18 requested) atoms. Cycle 25: After refmac, R = 0.2440 (Rfree = 0.000) for 4075 atoms. Found 28 (36 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 2.37 Search for helices and strands: 0 residues in 0 chains, 4166 seeds are put forward NCS extension: 27 residues added (22 deleted due to clashes), 4193 seeds are put forward Round 1: 419 peptides, 38 chains. Longest chain 31 peptides. Score 0.626 Round 2: 428 peptides, 30 chains. Longest chain 36 peptides. Score 0.681 Round 3: 427 peptides, 34 chains. Longest chain 37 peptides. Score 0.658 Round 4: 419 peptides, 33 chains. Longest chain 42 peptides. Score 0.654 Round 5: 418 peptides, 36 chains. Longest chain 31 peptides. Score 0.636 Taking the results from Round 2 Chains 31, Residues 398, Estimated correctness of the model 61.0 % 9 chains (199 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6696 restraints for refining 4104 atoms. 4274 conditional restraints added. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2644 (Rfree = 0.000) for 4104 atoms. Found 36 (36 requested) and removed 25 (18 requested) atoms. Cycle 27: After refmac, R = 0.2410 (Rfree = 0.000) for 4093 atoms. Found 18 (36 requested) and removed 22 (18 requested) atoms. Cycle 28: After refmac, R = 0.2345 (Rfree = 0.000) for 4078 atoms. Found 13 (36 requested) and removed 19 (18 requested) atoms. Cycle 29: After refmac, R = 0.2295 (Rfree = 0.000) for 4067 atoms. Found 16 (36 requested) and removed 18 (18 requested) atoms. Cycle 30: After refmac, R = 0.2271 (Rfree = 0.000) for 4062 atoms. Found 10 (36 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 2.40 Search for helices and strands: 0 residues in 0 chains, 4182 seeds are put forward NCS extension: 31 residues added (10 deleted due to clashes), 4213 seeds are put forward Round 1: 415 peptides, 29 chains. Longest chain 46 peptides. Score 0.672 Round 2: 420 peptides, 28 chains. Longest chain 46 peptides. Score 0.683 Round 3: 424 peptides, 34 chains. Longest chain 51 peptides. Score 0.655 Round 4: 423 peptides, 36 chains. Longest chain 34 peptides. Score 0.642 Round 5: 413 peptides, 34 chains. Longest chain 46 peptides. Score 0.642 Taking the results from Round 2 Chains 33, Residues 392, Estimated correctness of the model 61.5 % 11 chains (256 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6459 restraints for refining 4192 atoms. 3819 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2667 (Rfree = 0.000) for 4192 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. Cycle 32: After refmac, R = 0.2419 (Rfree = 0.000) for 4184 atoms. Found 18 (37 requested) and removed 19 (18 requested) atoms. Cycle 33: After refmac, R = 0.2344 (Rfree = 0.000) for 4173 atoms. Found 12 (37 requested) and removed 19 (18 requested) atoms. Cycle 34: After refmac, R = 0.2582 (Rfree = 0.000) for 4160 atoms. Found 37 (37 requested) and removed 18 (18 requested) atoms. Cycle 35: After refmac, R = 0.2275 (Rfree = 0.000) for 4170 atoms. Found 13 (37 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 2.43 Search for helices and strands: 0 residues in 0 chains, 4263 seeds are put forward NCS extension: 15 residues added (19 deleted due to clashes), 4278 seeds are put forward Round 1: 406 peptides, 31 chains. Longest chain 46 peptides. Score 0.651 Round 2: 425 peptides, 30 chains. Longest chain 54 peptides. Score 0.678 Round 3: 425 peptides, 27 chains. Longest chain 57 peptides. Score 0.694 Round 4: 416 peptides, 37 chains. Longest chain 36 peptides. Score 0.628 Round 5: 425 peptides, 38 chains. Longest chain 55 peptides. Score 0.633 Taking the results from Round 3 Chains 28, Residues 398, Estimated correctness of the model 63.9 % 8 chains (237 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6496 restraints for refining 4154 atoms. 3953 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2638 (Rfree = 0.000) for 4154 atoms. Found 37 (37 requested) and removed 35 (18 requested) atoms. Cycle 37: After refmac, R = 0.2424 (Rfree = 0.000) for 4141 atoms. Found 25 (37 requested) and removed 21 (18 requested) atoms. Cycle 38: After refmac, R = 0.2342 (Rfree = 0.000) for 4132 atoms. Found 14 (37 requested) and removed 18 (18 requested) atoms. Cycle 39: After refmac, R = 0.2358 (Rfree = 0.000) for 4121 atoms. Found 22 (37 requested) and removed 18 (18 requested) atoms. Cycle 40: After refmac, R = 0.2568 (Rfree = 0.000) for 4115 atoms. Found 36 (36 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 2.40 Search for helices and strands: 0 residues in 0 chains, 4234 seeds are put forward NCS extension: 21 residues added (30 deleted due to clashes), 4255 seeds are put forward Round 1: 404 peptides, 36 chains. Longest chain 28 peptides. Score 0.619 Round 2: 415 peptides, 27 chains. Longest chain 50 peptides. Score 0.683 Round 3: 411 peptides, 34 chains. Longest chain 27 peptides. Score 0.640 Round 4: 415 peptides, 33 chains. Longest chain 35 peptides. Score 0.650 Round 5: 404 peptides, 30 chains. Longest chain 25 peptides. Score 0.654 Taking the results from Round 2 Chains 34, Residues 388, Estimated correctness of the model 61.5 % 12 chains (255 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6248 restraints for refining 4089 atoms. 3627 conditional restraints added. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2572 (Rfree = 0.000) for 4089 atoms. Found 36 (36 requested) and removed 27 (18 requested) atoms. Cycle 42: After refmac, R = 0.2620 (Rfree = 0.000) for 4079 atoms. Found 36 (36 requested) and removed 24 (18 requested) atoms. Cycle 43: After refmac, R = 0.2353 (Rfree = 0.000) for 4078 atoms. Found 32 (36 requested) and removed 21 (18 requested) atoms. Cycle 44: After refmac, R = 0.2234 (Rfree = 0.000) for 4074 atoms. Found 31 (36 requested) and removed 19 (18 requested) atoms. Cycle 45: After refmac, R = 0.2185 (Rfree = 0.000) for 4077 atoms. Found 27 (36 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 2.37 Search for helices and strands: 0 residues in 0 chains, 4199 seeds are put forward NCS extension: 18 residues added (18 deleted due to clashes), 4217 seeds are put forward Round 1: 410 peptides, 36 chains. Longest chain 42 peptides. Score 0.627 Round 2: 433 peptides, 34 chains. Longest chain 42 peptides. Score 0.665 Round 3: 414 peptides, 26 chains. Longest chain 39 peptides. Score 0.688 Round 4: 410 peptides, 34 chains. Longest chain 34 peptides. Score 0.638 Round 5: 436 peptides, 29 chains. Longest chain 33 peptides. Score 0.695 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 407, Estimated correctness of the model 64.1 % 12 chains (250 residues) have been docked in sequence Sequence coverage is 61 % Consider running further cycles of model building using 2avn-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 38 A and 47 A Built loop between residues 63 A and 72 A Built loop between residues 90 A and 94 A Built loop between residues 103 A and 106 A Built loop between residues 184 A and 187 A Built loop between residues 123 B and 136 B 20 chains (427 residues) following loop building 6 chains (285 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17047 reflections ( 99.73 % complete ) and 5784 restraints for refining 4139 atoms. 3036 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2943 (Rfree = 0.000) for 4139 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2756 (Rfree = 0.000) for 4086 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2661 (Rfree = 0.000) for 4048 atoms. Found 0 (36 requested) and removed 15 (18 requested) atoms. Cycle 49: After refmac, R = 0.2574 (Rfree = 0.000) for 4017 atoms. Found 0 (36 requested) and removed 8 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:51:18 GMT 2018 Job finished. TimeTaking 63.44 Used memory is bytes: 10642456