null Mon 24 Dec 00:44:27 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 2go7-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2go7-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2go7-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.6-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/2go7-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.6-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 ============================================================ Mon 24 Dec 00:44:32 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/2go7-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.6-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 810 and 0 Target number of residues in the AU: 810 Target solvent content: 0.6427 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 828 Adjusted target solvent content: 0.63 Input MTZ file: 2go7-3.6-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: 169 Cell parameters: 155.000 155.000 88.440 90.000 90.000 120.000 Input sequence file: 2go7-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6624 target number of atoms Had to go as low as 1.10 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: 134.234 3.600 Wilson plot Bfac: 73.62 14169 reflections ( 99.78 % complete ) and 0 restraints for refining 7424 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3432 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3137 (Rfree = 0.000) for 7424 atoms. Found 47 (47 requested) and removed 37 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 2.92 Search for helices and strands: 0 residues in 0 chains, 7587 seeds are put forward NCS extension: 0 residues added, 7587 seeds are put forward Round 1: 389 peptides, 65 chains. Longest chain 15 peptides. Score 0.370 Round 2: 485 peptides, 66 chains. Longest chain 19 peptides. Score 0.489 Round 3: 529 peptides, 63 chains. Longest chain 26 peptides. Score 0.554 Round 4: 533 peptides, 61 chains. Longest chain 25 peptides. Score 0.569 Round 5: 553 peptides, 57 chains. Longest chain 23 peptides. Score 0.608 Taking the results from Round 5 Chains 60, Residues 496, Estimated correctness of the model 17.8 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 12724 restraints for refining 6000 atoms. 10710 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2707 (Rfree = 0.000) for 6000 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. Cycle 2: After refmac, R = 0.2599 (Rfree = 0.000) for 5882 atoms. Found 26 (38 requested) and removed 29 (19 requested) atoms. Cycle 3: After refmac, R = 0.2470 (Rfree = 0.000) for 5840 atoms. Found 16 (37 requested) and removed 26 (18 requested) atoms. Cycle 4: After refmac, R = 0.2360 (Rfree = 0.000) for 5808 atoms. Found 10 (37 requested) and removed 22 (18 requested) atoms. Cycle 5: After refmac, R = 0.2321 (Rfree = 0.000) for 5782 atoms. Found 10 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 2.89 Search for helices and strands: 0 residues in 0 chains, 6046 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 6063 seeds are put forward Round 1: 511 peptides, 69 chains. Longest chain 33 peptides. Score 0.503 Round 2: 541 peptides, 63 chains. Longest chain 23 peptides. Score 0.567 Round 3: 557 peptides, 59 chains. Longest chain 31 peptides. Score 0.603 Round 4: 530 peptides, 58 chains. Longest chain 27 peptides. Score 0.580 Round 5: 541 peptides, 65 chains. Longest chain 24 peptides. Score 0.557 Taking the results from Round 3 Chains 63, Residues 498, Estimated correctness of the model 15.8 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 12636 restraints for refining 6004 atoms. 10579 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2560 (Rfree = 0.000) for 6004 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 7: After refmac, R = 0.2358 (Rfree = 0.000) for 5976 atoms. Found 13 (38 requested) and removed 23 (19 requested) atoms. Cycle 8: After refmac, R = 0.2291 (Rfree = 0.000) for 5940 atoms. Found 10 (38 requested) and removed 23 (19 requested) atoms. Cycle 9: After refmac, R = 0.2235 (Rfree = 0.000) for 5914 atoms. Found 17 (38 requested) and removed 20 (19 requested) atoms. Cycle 10: After refmac, R = 0.2198 (Rfree = 0.000) for 5900 atoms. Found 8 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 2.89 Search for helices and strands: 0 residues in 0 chains, 6152 seeds are put forward NCS extension: 22 residues added (8 deleted due to clashes), 6174 seeds are put forward Round 1: 503 peptides, 69 chains. Longest chain 26 peptides. Score 0.494 Round 2: 547 peptides, 66 chains. Longest chain 31 peptides. Score 0.559 Round 3: 528 peptides, 58 chains. Longest chain 23 peptides. Score 0.578 Round 4: 545 peptides, 66 chains. Longest chain 22 peptides. Score 0.557 Round 5: 543 peptides, 60 chains. Longest chain 26 peptides. Score 0.584 Taking the results from Round 5 Chains 62, Residues 483, Estimated correctness of the model 8.3 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13037 restraints for refining 6004 atoms. 11089 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2545 (Rfree = 0.000) for 6004 atoms. Found 35 (38 requested) and removed 29 (19 requested) atoms. Cycle 12: After refmac, R = 0.2283 (Rfree = 0.000) for 5971 atoms. Found 21 (38 requested) and removed 23 (19 requested) atoms. Cycle 13: After refmac, R = 0.2109 (Rfree = 0.000) for 5944 atoms. Found 12 (38 requested) and removed 27 (19 requested) atoms. Cycle 14: After refmac, R = 0.2038 (Rfree = 0.000) for 5917 atoms. Found 9 (38 requested) and removed 26 (19 requested) atoms. Cycle 15: After refmac, R = 0.2000 (Rfree = 0.000) for 5878 atoms. Found 14 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 2.85 Search for helices and strands: 0 residues in 0 chains, 6148 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 6181 seeds are put forward Round 1: 481 peptides, 71 chains. Longest chain 17 peptides. Score 0.456 Round 2: 519 peptides, 68 chains. Longest chain 16 peptides. Score 0.518 Round 3: 541 peptides, 67 chains. Longest chain 21 peptides. Score 0.547 Round 4: 537 peptides, 66 chains. Longest chain 22 peptides. Score 0.548 Round 5: 547 peptides, 63 chains. Longest chain 25 peptides. Score 0.574 Taking the results from Round 5 Chains 64, Residues 484, Estimated correctness of the model 4.2 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 12862 restraints for refining 6002 atoms. 10882 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2581 (Rfree = 0.000) for 6002 atoms. Found 38 (38 requested) and removed 30 (19 requested) atoms. Cycle 17: After refmac, R = 0.2118 (Rfree = 0.000) for 5949 atoms. Found 18 (38 requested) and removed 24 (19 requested) atoms. Cycle 18: After refmac, R = 0.2029 (Rfree = 0.000) for 5921 atoms. Found 8 (38 requested) and removed 28 (19 requested) atoms. Cycle 19: After refmac, R = 0.2061 (Rfree = 0.000) for 5890 atoms. Found 34 (37 requested) and removed 21 (18 requested) atoms. Cycle 20: After refmac, R = 0.1865 (Rfree = 0.000) for 5895 atoms. Found 10 (37 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 2.86 Search for helices and strands: 0 residues in 0 chains, 6193 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6206 seeds are put forward Round 1: 473 peptides, 75 chains. Longest chain 13 peptides. Score 0.424 Round 2: 519 peptides, 65 chains. Longest chain 22 peptides. Score 0.533 Round 3: 533 peptides, 63 chains. Longest chain 25 peptides. Score 0.559 Round 4: 539 peptides, 66 chains. Longest chain 21 peptides. Score 0.550 Round 5: 526 peptides, 65 chains. Longest chain 31 peptides. Score 0.541 Taking the results from Round 3 Chains 63, Residues 470, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 12988 restraints for refining 6004 atoms. 11134 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2356 (Rfree = 0.000) for 6004 atoms. Found 38 (38 requested) and removed 30 (19 requested) atoms. Cycle 22: After refmac, R = 0.2247 (Rfree = 0.000) for 5981 atoms. Found 31 (38 requested) and removed 29 (19 requested) atoms. Cycle 23: After refmac, R = 0.2100 (Rfree = 0.000) for 5959 atoms. Found 22 (38 requested) and removed 27 (19 requested) atoms. Cycle 24: After refmac, R = 0.1959 (Rfree = 0.000) for 5937 atoms. Found 19 (38 requested) and removed 23 (19 requested) atoms. Cycle 25: After refmac, R = 0.1906 (Rfree = 0.000) for 5916 atoms. Found 15 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 2.86 Search for helices and strands: 0 residues in 0 chains, 6167 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 6187 seeds are put forward Round 1: 470 peptides, 70 chains. Longest chain 17 peptides. Score 0.448 Round 2: 522 peptides, 73 chains. Longest chain 24 peptides. Score 0.495 Round 3: 530 peptides, 67 chains. Longest chain 20 peptides. Score 0.535 Round 4: 519 peptides, 65 chains. Longest chain 19 peptides. Score 0.533 Round 5: 519 peptides, 62 chains. Longest chain 30 peptides. Score 0.548 Taking the results from Round 5 Chains 64, Residues 457, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13060 restraints for refining 6004 atoms. 11250 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2284 (Rfree = 0.000) for 6004 atoms. Found 38 (38 requested) and removed 30 (19 requested) atoms. Cycle 27: After refmac, R = 0.2096 (Rfree = 0.000) for 5970 atoms. Found 20 (38 requested) and removed 22 (19 requested) atoms. Cycle 28: After refmac, R = 0.2148 (Rfree = 0.000) for 5942 atoms. Found 31 (38 requested) and removed 28 (19 requested) atoms. Cycle 29: After refmac, R = 0.1900 (Rfree = 0.000) for 5925 atoms. Found 13 (38 requested) and removed 22 (19 requested) atoms. Cycle 30: After refmac, R = 0.1911 (Rfree = 0.000) for 5901 atoms. Found 11 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 2.88 Search for helices and strands: 0 residues in 0 chains, 6125 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 6145 seeds are put forward Round 1: 446 peptides, 74 chains. Longest chain 16 peptides. Score 0.394 Round 2: 477 peptides, 63 chains. Longest chain 29 peptides. Score 0.495 Round 3: 501 peptides, 61 chains. Longest chain 22 peptides. Score 0.534 Round 4: 518 peptides, 64 chains. Longest chain 29 peptides. Score 0.537 Round 5: 521 peptides, 66 chains. Longest chain 19 peptides. Score 0.530 Taking the results from Round 4 Chains 66, Residues 454, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13006 restraints for refining 6003 atoms. 11179 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2309 (Rfree = 0.000) for 6003 atoms. Found 25 (38 requested) and removed 27 (19 requested) atoms. Cycle 32: After refmac, R = 0.2089 (Rfree = 0.000) for 5968 atoms. Found 14 (38 requested) and removed 24 (19 requested) atoms. Cycle 33: After refmac, R = 0.2011 (Rfree = 0.000) for 5935 atoms. Found 9 (38 requested) and removed 27 (19 requested) atoms. Cycle 34: After refmac, R = 0.1965 (Rfree = 0.000) for 5896 atoms. Found 8 (37 requested) and removed 21 (18 requested) atoms. Cycle 35: After refmac, R = 0.1841 (Rfree = 0.000) for 5865 atoms. Found 6 (37 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 2.84 Search for helices and strands: 0 residues in 0 chains, 6060 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6079 seeds are put forward Round 1: 482 peptides, 78 chains. Longest chain 18 peptides. Score 0.418 Round 2: 532 peptides, 70 chains. Longest chain 29 peptides. Score 0.522 Round 3: 522 peptides, 66 chains. Longest chain 21 peptides. Score 0.531 Round 4: 524 peptides, 66 chains. Longest chain 21 peptides. Score 0.534 Round 5: 523 peptides, 65 chains. Longest chain 29 peptides. Score 0.538 Taking the results from Round 5 Chains 65, Residues 458, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13043 restraints for refining 6002 atoms. 11276 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2497 (Rfree = 0.000) for 6002 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 37: After refmac, R = 0.2384 (Rfree = 0.000) for 5973 atoms. Found 38 (38 requested) and removed 52 (19 requested) atoms. Cycle 38: After refmac, R = 0.2045 (Rfree = 0.000) for 5928 atoms. Found 24 (38 requested) and removed 42 (19 requested) atoms. Cycle 39: After refmac, R = 0.2090 (Rfree = 0.000) for 5900 atoms. Found 29 (37 requested) and removed 29 (18 requested) atoms. Cycle 40: After refmac, R = 0.1921 (Rfree = 0.000) for 5882 atoms. Found 20 (37 requested) and removed 30 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 2.84 Search for helices and strands: 0 residues in 0 chains, 6173 seeds are put forward NCS extension: 20 residues added (7 deleted due to clashes), 6193 seeds are put forward Round 1: 425 peptides, 77 chains. Longest chain 14 peptides. Score 0.347 Round 2: 453 peptides, 72 chains. Longest chain 18 peptides. Score 0.415 Round 3: 475 peptides, 63 chains. Longest chain 21 peptides. Score 0.493 Round 4: 503 peptides, 66 chains. Longest chain 24 peptides. Score 0.510 Round 5: 488 peptides, 68 chains. Longest chain 20 peptides. Score 0.481 Taking the results from Round 4 Chains 69, Residues 437, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13044 restraints for refining 6004 atoms. 11288 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2435 (Rfree = 0.000) for 6004 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. Cycle 42: After refmac, R = 0.2092 (Rfree = 0.000) for 5992 atoms. Found 25 (38 requested) and removed 36 (19 requested) atoms. Cycle 43: After refmac, R = 0.2014 (Rfree = 0.000) for 5967 atoms. Found 22 (38 requested) and removed 25 (19 requested) atoms. Cycle 44: After refmac, R = 0.1968 (Rfree = 0.000) for 5955 atoms. Found 24 (38 requested) and removed 31 (19 requested) atoms. Cycle 45: After refmac, R = 0.1875 (Rfree = 0.000) for 5940 atoms. Found 19 (38 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 2.83 Search for helices and strands: 0 residues in 0 chains, 6186 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 6199 seeds are put forward Round 1: 417 peptides, 69 chains. Longest chain 15 peptides. Score 0.385 Round 2: 473 peptides, 67 chains. Longest chain 17 peptides. Score 0.469 Round 3: 484 peptides, 66 chains. Longest chain 23 peptides. Score 0.487 Round 4: 490 peptides, 66 chains. Longest chain 18 peptides. Score 0.495 Round 5: 488 peptides, 61 chains. Longest chain 18 peptides. Score 0.519 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 63, Residues 427, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2go7-3_warpNtrace.pdb as input Building loops using Loopy2018 63 chains (427 residues) following loop building 4 chains (33 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14169 reflections ( 99.78 % complete ) and 12758 restraints for refining 6002 atoms. 10985 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2182 (Rfree = 0.000) for 6002 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.1993 (Rfree = 0.000) for 5966 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2048 (Rfree = 0.000) for 5938 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.2077 (Rfree = 0.000) for 5913 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:00:20 GMT 2018 Job finished. TimeTaking 75.87 Used memory is bytes: 11312952