Mon 24 Dec 01:00:28 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 1vpm-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vpm-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vpm-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-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/1vpm-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-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 01:00:34 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/1vpm-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-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 350 and 0 Target number of residues in the AU: 350 Target solvent content: 0.6431 Checking the provided sequence file Detected sequence length: 169 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 507 Adjusted target solvent content: 0.48 Input MTZ file: 1vpm-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: 24 Cell parameters: 82.941 106.484 120.177 90.000 90.000 90.000 Input sequence file: 1vpm-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4056 target number of atoms Had to go as low as 0.55 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: 79.699 3.400 Wilson plot Bfac: 73.82 7484 reflections ( 98.11 % complete ) and 0 restraints for refining 4486 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3102 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2508 (Rfree = 0.000) for 4486 atoms. Found 30 (33 requested) and removed 65 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 4517 seeds are put forward NCS extension: 0 residues added, 4517 seeds are put forward Round 1: 232 peptides, 36 chains. Longest chain 16 peptides. Score 0.458 Round 2: 307 peptides, 33 chains. Longest chain 27 peptides. Score 0.668 Round 3: 322 peptides, 36 chains. Longest chain 33 peptides. Score 0.670 Round 4: 321 peptides, 32 chains. Longest chain 28 peptides. Score 0.703 Round 5: 332 peptides, 31 chains. Longest chain 39 peptides. Score 0.729 Taking the results from Round 5 Chains 35, Residues 301, Estimated correctness of the model 65.0 % 4 chains (42 residues) have been docked in sequence Building loops using Loopy2018 35 chains (301 residues) following loop building 4 chains (42 residues) in sequence following loop building ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7725 restraints for refining 3683 atoms. 6430 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2437 (Rfree = 0.000) for 3683 atoms. Found 27 (27 requested) and removed 50 (13 requested) atoms. Cycle 2: After refmac, R = 0.2214 (Rfree = 0.000) for 3624 atoms. Found 12 (26 requested) and removed 22 (13 requested) atoms. Cycle 3: After refmac, R = 0.2138 (Rfree = 0.000) for 3590 atoms. Found 11 (26 requested) and removed 18 (13 requested) atoms. Cycle 4: After refmac, R = 0.2050 (Rfree = 0.000) for 3571 atoms. Found 7 (25 requested) and removed 17 (13 requested) atoms. Cycle 5: After refmac, R = 0.1990 (Rfree = 0.000) for 3550 atoms. Found 7 (24 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 3651 seeds are put forward NCS extension: 45 residues added (4 deleted due to clashes), 3696 seeds are put forward Round 1: 312 peptides, 40 chains. Longest chain 25 peptides. Score 0.613 Round 2: 316 peptides, 31 chains. Longest chain 28 peptides. Score 0.702 Round 3: 331 peptides, 29 chains. Longest chain 51 peptides. Score 0.743 Round 4: 334 peptides, 33 chains. Longest chain 61 peptides. Score 0.717 Round 5: 354 peptides, 27 chains. Longest chain 39 peptides. Score 0.789 Taking the results from Round 5 Chains 34, Residues 327, Estimated correctness of the model 77.9 % 6 chains (105 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 B and 63 B 33 chains (331 residues) following loop building 5 chains (111 residues) in sequence following loop building ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 6917 restraints for refining 3688 atoms. 5283 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2370 (Rfree = 0.000) for 3688 atoms. Found 17 (24 requested) and removed 43 (13 requested) atoms. Cycle 7: After refmac, R = 0.2136 (Rfree = 0.000) for 3636 atoms. Found 6 (24 requested) and removed 21 (13 requested) atoms. Cycle 8: After refmac, R = 0.2071 (Rfree = 0.000) for 3610 atoms. Found 5 (23 requested) and removed 15 (13 requested) atoms. Cycle 9: After refmac, R = 0.2052 (Rfree = 0.000) for 3587 atoms. Found 6 (23 requested) and removed 16 (13 requested) atoms. Cycle 10: After refmac, R = 0.1966 (Rfree = 0.000) for 3572 atoms. Found 3 (22 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 3679 seeds are put forward NCS extension: 31 residues added (15 deleted due to clashes), 3710 seeds are put forward Round 1: 303 peptides, 33 chains. Longest chain 27 peptides. Score 0.660 Round 2: 328 peptides, 34 chains. Longest chain 48 peptides. Score 0.698 Round 3: 347 peptides, 35 chains. Longest chain 39 peptides. Score 0.723 Round 4: 324 peptides, 33 chains. Longest chain 35 peptides. Score 0.700 Round 5: 341 peptides, 37 chains. Longest chain 34 peptides. Score 0.697 Taking the results from Round 3 Chains 40, Residues 312, Estimated correctness of the model 63.6 % 6 chains (100 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 60 A 37 chains (312 residues) following loop building 5 chains (107 residues) in sequence following loop building ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7175 restraints for refining 3688 atoms. 5660 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2277 (Rfree = 0.000) for 3688 atoms. Found 21 (22 requested) and removed 32 (13 requested) atoms. Cycle 12: After refmac, R = 0.2119 (Rfree = 0.000) for 3660 atoms. Found 13 (21 requested) and removed 19 (13 requested) atoms. Cycle 13: After refmac, R = 0.1987 (Rfree = 0.000) for 3647 atoms. Found 6 (21 requested) and removed 18 (13 requested) atoms. Cycle 14: After refmac, R = 0.1920 (Rfree = 0.000) for 3632 atoms. Found 4 (20 requested) and removed 15 (13 requested) atoms. Cycle 15: After refmac, R = 0.1865 (Rfree = 0.000) for 3617 atoms. Found 7 (19 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 3729 seeds are put forward NCS extension: 27 residues added (27 deleted due to clashes), 3756 seeds are put forward Round 1: 309 peptides, 40 chains. Longest chain 21 peptides. Score 0.607 Round 2: 330 peptides, 37 chains. Longest chain 33 peptides. Score 0.677 Round 3: 323 peptides, 31 chains. Longest chain 33 peptides. Score 0.714 Round 4: 312 peptides, 34 chains. Longest chain 31 peptides. Score 0.669 Round 5: 314 peptides, 32 chains. Longest chain 34 peptides. Score 0.690 Taking the results from Round 3 Chains 35, Residues 292, Estimated correctness of the model 61.4 % 4 chains (64 residues) have been docked in sequence Building loops using Loopy2018 35 chains (292 residues) following loop building 4 chains (64 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 7484 reflections ( 98.11 % complete ) and 7509 restraints for refining 3687 atoms. 6148 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2149 (Rfree = 0.000) for 3687 atoms. Found 12 (19 requested) and removed 30 (13 requested) atoms. Cycle 17: After refmac, R = 0.2056 (Rfree = 0.000) for 3654 atoms. Found 8 (18 requested) and removed 13 (13 requested) atoms. Cycle 18: After refmac, R = 0.2058 (Rfree = 0.000) for 3646 atoms. Found 12 (18 requested) and removed 13 (13 requested) atoms. Cycle 19: After refmac, R = 0.2017 (Rfree = 0.000) for 3636 atoms. Found 9 (17 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.1994 (Rfree = 0.000) for 3627 atoms. Found 6 (17 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 3719 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 3742 seeds are put forward Round 1: 292 peptides, 36 chains. Longest chain 38 peptides. Score 0.609 Round 2: 310 peptides, 35 chains. Longest chain 38 peptides. Score 0.656 Round 3: 317 peptides, 33 chains. Longest chain 50 peptides. Score 0.687 Round 4: 317 peptides, 30 chains. Longest chain 50 peptides. Score 0.712 Round 5: 315 peptides, 30 chains. Longest chain 34 peptides. Score 0.709 Taking the results from Round 4 Chains 32, Residues 287, Estimated correctness of the model 60.9 % 2 chains (61 residues) have been docked in sequence Building loops using Loopy2018 32 chains (287 residues) following loop building 2 chains (61 residues) in sequence following loop building ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7605 restraints for refining 3688 atoms. 6273 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2223 (Rfree = 0.000) for 3688 atoms. Found 15 (16 requested) and removed 22 (13 requested) atoms. Cycle 22: After refmac, R = 0.2123 (Rfree = 0.000) for 3671 atoms. Found 9 (16 requested) and removed 17 (13 requested) atoms. Cycle 23: After refmac, R = 0.2168 (Rfree = 0.000) for 3655 atoms. Found 11 (15 requested) and removed 16 (13 requested) atoms. Cycle 24: After refmac, R = 0.2013 (Rfree = 0.000) for 3646 atoms. Found 12 (15 requested) and removed 13 (13 requested) atoms. Cycle 25: After refmac, R = 0.1969 (Rfree = 0.000) for 3638 atoms. Found 12 (14 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 3750 seeds are put forward NCS extension: 76 residues added (4 deleted due to clashes), 3826 seeds are put forward Round 1: 285 peptides, 37 chains. Longest chain 21 peptides. Score 0.583 Round 2: 311 peptides, 34 chains. Longest chain 29 peptides. Score 0.667 Round 3: 303 peptides, 37 chains. Longest chain 28 peptides. Score 0.623 Round 4: 316 peptides, 34 chains. Longest chain 36 peptides. Score 0.676 Round 5: 302 peptides, 38 chains. Longest chain 19 peptides. Score 0.611 Taking the results from Round 4 Chains 34, Residues 282, Estimated correctness of the model 51.5 % 1 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 8067 restraints for refining 3688 atoms. 6865 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2100 (Rfree = 0.000) for 3688 atoms. Found 13 (13 requested) and removed 33 (13 requested) atoms. Cycle 27: After refmac, R = 0.1991 (Rfree = 0.000) for 3656 atoms. Found 10 (13 requested) and removed 23 (13 requested) atoms. Cycle 28: After refmac, R = 0.2016 (Rfree = 0.000) for 3641 atoms. Found 8 (13 requested) and removed 26 (13 requested) atoms. Cycle 29: After refmac, R = 0.1936 (Rfree = 0.000) for 3621 atoms. Found 9 (13 requested) and removed 23 (13 requested) atoms. Cycle 30: After refmac, R = 0.1957 (Rfree = 0.000) for 3607 atoms. Found 13 (13 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 3707 seeds are put forward NCS extension: 34 residues added (8 deleted due to clashes), 3741 seeds are put forward Round 1: 270 peptides, 42 chains. Longest chain 12 peptides. Score 0.490 Round 2: 272 peptides, 31 chains. Longest chain 31 peptides. Score 0.615 Round 3: 293 peptides, 35 chains. Longest chain 15 peptides. Score 0.621 Round 4: 287 peptides, 33 chains. Longest chain 24 peptides. Score 0.628 Round 5: 274 peptides, 34 chains. Longest chain 18 peptides. Score 0.589 Taking the results from Round 4 Chains 34, Residues 254, Estimated correctness of the model 37.5 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 8119 restraints for refining 3687 atoms. 7079 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2063 (Rfree = 0.000) for 3687 atoms. Found 13 (13 requested) and removed 22 (13 requested) atoms. Cycle 32: After refmac, R = 0.2001 (Rfree = 0.000) for 3674 atoms. Found 13 (13 requested) and removed 20 (13 requested) atoms. Cycle 33: After refmac, R = 0.1916 (Rfree = 0.000) for 3663 atoms. Found 13 (13 requested) and removed 17 (13 requested) atoms. Cycle 34: After refmac, R = 0.1945 (Rfree = 0.000) for 3656 atoms. Found 13 (13 requested) and removed 22 (13 requested) atoms. Cycle 35: After refmac, R = 0.1677 (Rfree = 0.000) for 3643 atoms. Found 11 (13 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 3758 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3772 seeds are put forward Round 1: 256 peptides, 44 chains. Longest chain 12 peptides. Score 0.427 Round 2: 281 peptides, 37 chains. Longest chain 17 peptides. Score 0.573 Round 3: 287 peptides, 40 chains. Longest chain 19 peptides. Score 0.556 Round 4: 297 peptides, 35 chains. Longest chain 19 peptides. Score 0.629 Round 5: 284 peptides, 35 chains. Longest chain 21 peptides. Score 0.601 Taking the results from Round 4 Chains 35, Residues 262, Estimated correctness of the model 37.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 8196 restraints for refining 3688 atoms. 7183 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2189 (Rfree = 0.000) for 3688 atoms. Found 13 (13 requested) and removed 19 (13 requested) atoms. Cycle 37: After refmac, R = 0.2056 (Rfree = 0.000) for 3677 atoms. Found 13 (13 requested) and removed 21 (13 requested) atoms. Cycle 38: After refmac, R = 0.1899 (Rfree = 0.000) for 3668 atoms. Found 13 (13 requested) and removed 14 (13 requested) atoms. Cycle 39: After refmac, R = 0.1901 (Rfree = 0.000) for 3665 atoms. Found 11 (13 requested) and removed 14 (13 requested) atoms. Cycle 40: After refmac, R = 0.1664 (Rfree = 0.000) for 3656 atoms. Found 5 (13 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 3761 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3787 seeds are put forward Round 1: 235 peptides, 36 chains. Longest chain 17 peptides. Score 0.466 Round 2: 255 peptides, 31 chains. Longest chain 20 peptides. Score 0.576 Round 3: 275 peptides, 36 chains. Longest chain 17 peptides. Score 0.570 Round 4: 272 peptides, 36 chains. Longest chain 19 peptides. Score 0.563 Round 5: 279 peptides, 36 chains. Longest chain 16 peptides. Score 0.579 Taking the results from Round 5 Chains 36, Residues 243, Estimated correctness of the model 21.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 8436 restraints for refining 3688 atoms. 7500 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2079 (Rfree = 0.000) for 3688 atoms. Found 13 (13 requested) and removed 25 (13 requested) atoms. Cycle 42: After refmac, R = 0.1975 (Rfree = 0.000) for 3673 atoms. Found 13 (13 requested) and removed 14 (13 requested) atoms. Cycle 43: After refmac, R = 0.1961 (Rfree = 0.000) for 3666 atoms. Found 13 (13 requested) and removed 15 (13 requested) atoms. Cycle 44: After refmac, R = 0.1867 (Rfree = 0.000) for 3659 atoms. Found 10 (13 requested) and removed 16 (13 requested) atoms. Cycle 45: After refmac, R = 0.1827 (Rfree = 0.000) for 3648 atoms. Found 13 (13 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 3758 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3773 seeds are put forward Round 1: 203 peptides, 33 chains. Longest chain 20 peptides. Score 0.412 Round 2: 236 peptides, 36 chains. Longest chain 14 peptides. Score 0.469 Round 3: 249 peptides, 34 chains. Longest chain 14 peptides. Score 0.528 Round 4: 243 peptides, 34 chains. Longest chain 17 peptides. Score 0.512 Round 5: 235 peptides, 32 chains. Longest chain 26 peptides. Score 0.515 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 215, Estimated correctness of the model 3.4 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vpm-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7484 reflections ( 98.11 % complete ) and 8458 restraints for refining 3688 atoms. 7632 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2029 (Rfree = 0.000) for 3688 atoms. Found 0 (13 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1959 (Rfree = 0.000) for 3667 atoms. Found 0 (13 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1937 (Rfree = 0.000) for 3653 atoms. Found 0 (13 requested) and removed 9 (13 requested) atoms. Cycle 49: After refmac, R = 0.1664 (Rfree = 0.000) for 3642 atoms. TimeTaking 53.22