null Mon 24 Dec 01:00:55 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 2go7-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2go7-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2go7-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.4-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/2go7-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.4-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 01:00:59 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/2go7-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.4-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 837 and 0 Target number of residues in the AU: 837 Target solvent content: 0.6307 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: 2go7-3.4-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: 2go7-3.4-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 3.400 Wilson plot Bfac: 66.73 16795 reflections ( 99.81 % complete ) and 0 restraints for refining 7388 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3410 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2906 (Rfree = 0.000) for 7388 atoms. Found 55 (55 requested) and removed 99 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 2.73 Search for helices and strands: 0 residues in 0 chains, 7493 seeds are put forward NCS extension: 0 residues added, 7493 seeds are put forward Round 1: 408 peptides, 78 chains. Longest chain 12 peptides. Score 0.317 Round 2: 506 peptides, 73 chains. Longest chain 20 peptides. Score 0.476 Round 3: 545 peptides, 74 chains. Longest chain 22 peptides. Score 0.517 Round 4: 565 peptides, 70 chains. Longest chain 23 peptides. Score 0.559 Round 5: 579 peptides, 61 chains. Longest chain 29 peptides. Score 0.615 Taking the results from Round 5 Chains 63, Residues 518, Estimated correctness of the model 33.5 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12364 restraints for refining 6020 atoms. 10218 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2704 (Rfree = 0.000) for 6020 atoms. Found 45 (45 requested) and removed 42 (22 requested) atoms. Cycle 2: After refmac, R = 0.2492 (Rfree = 0.000) for 5946 atoms. Found 26 (45 requested) and removed 26 (22 requested) atoms. Cycle 3: After refmac, R = 0.2401 (Rfree = 0.000) for 5917 atoms. Found 18 (44 requested) and removed 33 (22 requested) atoms. Cycle 4: After refmac, R = 0.2352 (Rfree = 0.000) for 5893 atoms. Found 16 (44 requested) and removed 27 (22 requested) atoms. Cycle 5: After refmac, R = 0.2282 (Rfree = 0.000) for 5876 atoms. Found 11 (44 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 2.76 Search for helices and strands: 0 residues in 0 chains, 6112 seeds are put forward NCS extension: 26 residues added (8 deleted due to clashes), 6138 seeds are put forward Round 1: 552 peptides, 74 chains. Longest chain 22 peptides. Score 0.525 Round 2: 585 peptides, 57 chains. Longest chain 34 peptides. Score 0.638 Round 3: 584 peptides, 60 chains. Longest chain 44 peptides. Score 0.624 Round 4: 571 peptides, 57 chains. Longest chain 48 peptides. Score 0.625 Round 5: 574 peptides, 59 chains. Longest chain 31 peptides. Score 0.619 Taking the results from Round 2 Chains 60, Residues 528, Estimated correctness of the model 40.6 % 5 chains (54 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12278 restraints for refining 6023 atoms. 10014 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2579 (Rfree = 0.000) for 6023 atoms. Found 45 (45 requested) and removed 34 (22 requested) atoms. Cycle 7: After refmac, R = 0.2373 (Rfree = 0.000) for 6011 atoms. Found 19 (45 requested) and removed 27 (22 requested) atoms. Cycle 8: After refmac, R = 0.2299 (Rfree = 0.000) for 5985 atoms. Found 11 (45 requested) and removed 23 (22 requested) atoms. Cycle 9: After refmac, R = 0.2225 (Rfree = 0.000) for 5959 atoms. Found 9 (45 requested) and removed 25 (22 requested) atoms. Cycle 10: After refmac, R = 0.2178 (Rfree = 0.000) for 5931 atoms. Found 6 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 2.76 Search for helices and strands: 0 residues in 0 chains, 6155 seeds are put forward NCS extension: 11 residues added (9 deleted due to clashes), 6166 seeds are put forward Round 1: 540 peptides, 63 chains. Longest chain 28 peptides. Score 0.566 Round 2: 584 peptides, 63 chains. Longest chain 33 peptides. Score 0.611 Round 3: 580 peptides, 60 chains. Longest chain 27 peptides. Score 0.620 Round 4: 593 peptides, 64 chains. Longest chain 24 peptides. Score 0.615 Round 5: 571 peptides, 56 chains. Longest chain 33 peptides. Score 0.630 Taking the results from Round 5 Chains 60, Residues 515, Estimated correctness of the model 38.2 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12721 restraints for refining 6022 atoms. 10547 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2520 (Rfree = 0.000) for 6022 atoms. Found 36 (45 requested) and removed 32 (22 requested) atoms. Cycle 12: After refmac, R = 0.2293 (Rfree = 0.000) for 5995 atoms. Found 19 (45 requested) and removed 25 (22 requested) atoms. Cycle 13: After refmac, R = 0.2192 (Rfree = 0.000) for 5964 atoms. Found 21 (45 requested) and removed 24 (22 requested) atoms. Cycle 14: After refmac, R = 0.2134 (Rfree = 0.000) for 5944 atoms. Found 10 (45 requested) and removed 24 (22 requested) atoms. Cycle 15: After refmac, R = 0.2085 (Rfree = 0.000) for 5923 atoms. Found 7 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 2.74 Search for helices and strands: 0 residues in 0 chains, 6154 seeds are put forward NCS extension: 27 residues added (9 deleted due to clashes), 6181 seeds are put forward Round 1: 533 peptides, 69 chains. Longest chain 22 peptides. Score 0.529 Round 2: 575 peptides, 60 chains. Longest chain 49 peptides. Score 0.616 Round 3: 586 peptides, 61 chains. Longest chain 45 peptides. Score 0.622 Round 4: 589 peptides, 64 chains. Longest chain 28 peptides. Score 0.611 Round 5: 601 peptides, 57 chains. Longest chain 51 peptides. Score 0.653 Taking the results from Round 5 Chains 68, Residues 544, Estimated correctness of the model 45.0 % 8 chains (116 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 11724 restraints for refining 6021 atoms. 9139 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2498 (Rfree = 0.000) for 6021 atoms. Found 44 (45 requested) and removed 40 (22 requested) atoms. Cycle 17: After refmac, R = 0.2274 (Rfree = 0.000) for 5990 atoms. Found 16 (45 requested) and removed 27 (22 requested) atoms. Cycle 18: After refmac, R = 0.2212 (Rfree = 0.000) for 5956 atoms. Found 22 (45 requested) and removed 29 (22 requested) atoms. Cycle 19: After refmac, R = 0.2084 (Rfree = 0.000) for 5925 atoms. Found 10 (44 requested) and removed 26 (22 requested) atoms. Cycle 20: After refmac, R = 0.2043 (Rfree = 0.000) for 5900 atoms. Found 13 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 2.75 Search for helices and strands: 0 residues in 0 chains, 6147 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 6159 seeds are put forward Round 1: 560 peptides, 72 chains. Longest chain 25 peptides. Score 0.543 Round 2: 588 peptides, 57 chains. Longest chain 41 peptides. Score 0.641 Round 3: 585 peptides, 64 chains. Longest chain 30 peptides. Score 0.607 Round 4: 591 peptides, 58 chains. Longest chain 46 peptides. Score 0.640 Round 5: 581 peptides, 62 chains. Longest chain 29 peptides. Score 0.612 Taking the results from Round 2 Chains 60, Residues 531, Estimated correctness of the model 41.5 % 2 chains (52 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12286 restraints for refining 6022 atoms. 10003 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2319 (Rfree = 0.000) for 6022 atoms. Found 34 (45 requested) and removed 31 (22 requested) atoms. Cycle 22: After refmac, R = 0.2227 (Rfree = 0.000) for 6013 atoms. Found 15 (45 requested) and removed 23 (22 requested) atoms. Cycle 23: After refmac, R = 0.2050 (Rfree = 0.000) for 5994 atoms. Found 10 (45 requested) and removed 23 (22 requested) atoms. Cycle 24: After refmac, R = 0.2031 (Rfree = 0.000) for 5973 atoms. Found 11 (45 requested) and removed 23 (22 requested) atoms. Cycle 25: After refmac, R = 0.2032 (Rfree = 0.000) for 5956 atoms. Found 8 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 2.74 Search for helices and strands: 0 residues in 0 chains, 6188 seeds are put forward NCS extension: 33 residues added (15 deleted due to clashes), 6221 seeds are put forward Round 1: 523 peptides, 67 chains. Longest chain 23 peptides. Score 0.528 Round 2: 584 peptides, 64 chains. Longest chain 33 peptides. Score 0.606 Round 3: 587 peptides, 64 chains. Longest chain 28 peptides. Score 0.609 Round 4: 600 peptides, 71 chains. Longest chain 22 peptides. Score 0.590 Round 5: 599 peptides, 70 chains. Longest chain 23 peptides. Score 0.594 Taking the results from Round 3 Chains 64, Residues 523, Estimated correctness of the model 31.6 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12667 restraints for refining 6021 atoms. 10504 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2402 (Rfree = 0.000) for 6021 atoms. Found 41 (45 requested) and removed 24 (22 requested) atoms. Cycle 27: After refmac, R = 0.2253 (Rfree = 0.000) for 6022 atoms. Found 24 (45 requested) and removed 22 (22 requested) atoms. Cycle 28: After refmac, R = 0.2146 (Rfree = 0.000) for 6016 atoms. Found 12 (45 requested) and removed 22 (22 requested) atoms. Cycle 29: After refmac, R = 0.2138 (Rfree = 0.000) for 6001 atoms. Found 1 (45 requested) and removed 23 (22 requested) atoms. Cycle 30: After refmac, R = 0.2137 (Rfree = 0.000) for 5972 atoms. Found 8 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 2.76 Search for helices and strands: 0 residues in 0 chains, 6190 seeds are put forward NCS extension: 26 residues added (18 deleted due to clashes), 6216 seeds are put forward Round 1: 547 peptides, 76 chains. Longest chain 24 peptides. Score 0.509 Round 2: 556 peptides, 63 chains. Longest chain 28 peptides. Score 0.583 Round 3: 560 peptides, 65 chains. Longest chain 23 peptides. Score 0.577 Round 4: 586 peptides, 67 chains. Longest chain 26 peptides. Score 0.595 Round 5: 559 peptides, 61 chains. Longest chain 25 peptides. Score 0.595 Taking the results from Round 5 Chains 63, Residues 498, Estimated correctness of the model 27.0 % 5 chains (53 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12733 restraints for refining 6023 atoms. 10603 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2468 (Rfree = 0.000) for 6023 atoms. Found 45 (45 requested) and removed 27 (22 requested) atoms. Cycle 32: After refmac, R = 0.2271 (Rfree = 0.000) for 6022 atoms. Found 18 (45 requested) and removed 25 (22 requested) atoms. Cycle 33: After refmac, R = 0.2212 (Rfree = 0.000) for 6009 atoms. Found 7 (45 requested) and removed 25 (22 requested) atoms. Cycle 34: After refmac, R = 0.2178 (Rfree = 0.000) for 5977 atoms. Found 10 (45 requested) and removed 25 (22 requested) atoms. Cycle 35: After refmac, R = 0.2150 (Rfree = 0.000) for 5960 atoms. Found 4 (45 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 2.77 Search for helices and strands: 0 residues in 0 chains, 6153 seeds are put forward NCS extension: 24 residues added (7 deleted due to clashes), 6177 seeds are put forward Round 1: 493 peptides, 68 chains. Longest chain 19 peptides. Score 0.487 Round 2: 525 peptides, 63 chains. Longest chain 24 peptides. Score 0.550 Round 3: 539 peptides, 66 chains. Longest chain 24 peptides. Score 0.550 Round 4: 548 peptides, 65 chains. Longest chain 29 peptides. Score 0.565 Round 5: 558 peptides, 61 chains. Longest chain 27 peptides. Score 0.594 Taking the results from Round 5 Chains 64, Residues 497, Estimated correctness of the model 26.7 % 5 chains (71 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12421 restraints for refining 6022 atoms. 10215 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2456 (Rfree = 0.000) for 6022 atoms. Found 15 (45 requested) and removed 32 (22 requested) atoms. Cycle 37: After refmac, R = 0.2278 (Rfree = 0.000) for 5984 atoms. Found 12 (45 requested) and removed 29 (22 requested) atoms. Cycle 38: After refmac, R = 0.2237 (Rfree = 0.000) for 5957 atoms. Found 9 (45 requested) and removed 25 (22 requested) atoms. Cycle 39: After refmac, R = 0.2203 (Rfree = 0.000) for 5935 atoms. Found 7 (44 requested) and removed 23 (22 requested) atoms. Cycle 40: After refmac, R = 0.2145 (Rfree = 0.000) for 5912 atoms. Found 9 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 2.75 Search for helices and strands: 0 residues in 0 chains, 6133 seeds are put forward NCS extension: 8 residues added (7 deleted due to clashes), 6141 seeds are put forward Round 1: 483 peptides, 68 chains. Longest chain 24 peptides. Score 0.475 Round 2: 521 peptides, 63 chains. Longest chain 27 peptides. Score 0.546 Round 3: 517 peptides, 59 chains. Longest chain 46 peptides. Score 0.561 Round 4: 527 peptides, 66 chains. Longest chain 19 peptides. Score 0.537 Round 5: 530 peptides, 62 chains. Longest chain 28 peptides. Score 0.560 Taking the results from Round 3 Chains 63, Residues 458, Estimated correctness of the model 15.4 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12884 restraints for refining 6022 atoms. 11004 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2376 (Rfree = 0.000) for 6022 atoms. Found 39 (45 requested) and removed 32 (22 requested) atoms. Cycle 42: After refmac, R = 0.2197 (Rfree = 0.000) for 6010 atoms. Found 12 (45 requested) and removed 24 (22 requested) atoms. Cycle 43: After refmac, R = 0.2142 (Rfree = 0.000) for 5990 atoms. Found 9 (45 requested) and removed 24 (22 requested) atoms. Cycle 44: After refmac, R = 0.2132 (Rfree = 0.000) for 5971 atoms. Found 7 (45 requested) and removed 22 (22 requested) atoms. Cycle 45: After refmac, R = 0.2082 (Rfree = 0.000) for 5953 atoms. Found 4 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 2.76 Search for helices and strands: 0 residues in 0 chains, 6173 seeds are put forward NCS extension: 38 residues added (6 deleted due to clashes), 6211 seeds are put forward Round 1: 492 peptides, 77 chains. Longest chain 20 peptides. Score 0.437 Round 2: 509 peptides, 68 chains. Longest chain 31 peptides. Score 0.506 Round 3: 523 peptides, 62 chains. Longest chain 25 peptides. Score 0.553 Round 4: 529 peptides, 61 chains. Longest chain 30 peptides. Score 0.564 Round 5: 534 peptides, 61 chains. Longest chain 26 peptides. Score 0.570 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 63, Residues 473, Estimated correctness of the model 18.6 % 3 chains (29 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2go7-3_warpNtrace.pdb as input Building loops using Loopy2018 63 chains (473 residues) following loop building 3 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16795 reflections ( 99.81 % complete ) and 12923 restraints for refining 6022 atoms. 10985 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2421 (Rfree = 0.000) for 6022 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2308 (Rfree = 0.000) for 5985 atoms. Found 0 (45 requested) and removed 8 (22 requested) atoms. Cycle 48: After refmac, R = 0.2274 (Rfree = 0.000) for 5970 atoms. Found 0 (45 requested) and removed 1 (22 requested) atoms. Cycle 49: After refmac, R = 0.2255 (Rfree = 0.000) for 5963 atoms. Found 0 (45 requested) and removed 4 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:04:59 GMT 2018 Job finished. TimeTaking 64.07 Used memory is bytes: 14617784