null Mon 24 Dec 07:26:53 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 1vpm-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vpm-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vpm-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.4-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/1vpm-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.4-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 07:26:58 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/1vpm-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.4-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 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-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: 24 Cell parameters: 82.941 106.484 120.177 90.000 90.000 90.000 Input sequence file: 1vpm-3.4-parrot-noncs.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 4485 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3123 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2655 (Rfree = 0.000) for 4485 atoms. Found 31 (33 requested) and removed 63 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 4549 seeds are put forward NCS extension: 0 residues added, 4549 seeds are put forward Round 1: 242 peptides, 38 chains. Longest chain 16 peptides. Score 0.461 Round 2: 299 peptides, 32 chains. Longest chain 24 peptides. Score 0.662 Round 3: 306 peptides, 33 chains. Longest chain 20 peptides. Score 0.666 Round 4: 320 peptides, 28 chains. Longest chain 25 peptides. Score 0.733 Round 5: 328 peptides, 30 chains. Longest chain 34 peptides. Score 0.730 Taking the results from Round 4 Chains 32, Residues 292, Estimated correctness of the model 66.0 % 4 chains (61 residues) have been docked in sequence Building loops using Loopy2018 32 chains (292 residues) following loop building 4 chains (61 residues) in sequence following loop building ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7575 restraints for refining 3687 atoms. 6242 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2498 (Rfree = 0.000) for 3687 atoms. Found 17 (27 requested) and removed 53 (13 requested) atoms. Cycle 2: After refmac, R = 0.2400 (Rfree = 0.000) for 3582 atoms. Found 21 (26 requested) and removed 33 (13 requested) atoms. Cycle 3: After refmac, R = 0.2265 (Rfree = 0.000) for 3543 atoms. Found 14 (25 requested) and removed 29 (13 requested) atoms. Cycle 4: After refmac, R = 0.2234 (Rfree = 0.000) for 3510 atoms. Found 17 (24 requested) and removed 24 (13 requested) atoms. Cycle 5: After refmac, R = 0.2164 (Rfree = 0.000) for 3488 atoms. Found 16 (24 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 3648 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3665 seeds are put forward Round 1: 291 peptides, 36 chains. Longest chain 27 peptides. Score 0.607 Round 2: 339 peptides, 31 chains. Longest chain 34 peptides. Score 0.740 Round 3: 329 peptides, 32 chains. Longest chain 32 peptides. Score 0.716 Round 4: 324 peptides, 34 chains. Longest chain 33 peptides. Score 0.691 Round 5: 341 peptides, 33 chains. Longest chain 37 peptides. Score 0.728 Taking the results from Round 2 Chains 35, Residues 308, Estimated correctness of the model 67.6 % 2 chains (20 residues) have been docked in sequence Building loops using Loopy2018 35 chains (308 residues) following loop building 2 chains (20 residues) in sequence following loop building ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7329 restraints for refining 3491 atoms. 6069 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2209 (Rfree = 0.000) for 3491 atoms. Found 19 (23 requested) and removed 32 (13 requested) atoms. Cycle 7: After refmac, R = 0.2089 (Rfree = 0.000) for 3468 atoms. Found 8 (23 requested) and removed 26 (13 requested) atoms. Cycle 8: After refmac, R = 0.2026 (Rfree = 0.000) for 3439 atoms. Found 9 (22 requested) and removed 21 (13 requested) atoms. Cycle 9: After refmac, R = 0.1918 (Rfree = 0.000) for 3418 atoms. Found 11 (21 requested) and removed 16 (12 requested) atoms. Cycle 10: After refmac, R = 0.1860 (Rfree = 0.000) for 3407 atoms. Found 9 (20 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 3532 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3548 seeds are put forward Round 1: 282 peptides, 32 chains. Longest chain 19 peptides. Score 0.627 Round 2: 310 peptides, 31 chains. Longest chain 32 peptides. Score 0.691 Round 3: 315 peptides, 35 chains. Longest chain 26 peptides. Score 0.666 Round 4: 311 peptides, 28 chains. Longest chain 39 peptides. Score 0.718 Round 5: 304 peptides, 28 chains. Longest chain 26 peptides. Score 0.706 Taking the results from Round 4 Chains 31, Residues 283, Estimated correctness of the model 62.4 % 3 chains (63 residues) have been docked in sequence Building loops using Loopy2018 31 chains (283 residues) following loop building 3 chains (63 residues) in sequence following loop building ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7163 restraints for refining 3570 atoms. 5818 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2151 (Rfree = 0.000) for 3570 atoms. Found 20 (21 requested) and removed 26 (13 requested) atoms. Cycle 12: After refmac, R = 0.2033 (Rfree = 0.000) for 3545 atoms. Found 12 (20 requested) and removed 20 (13 requested) atoms. Cycle 13: After refmac, R = 0.1948 (Rfree = 0.000) for 3532 atoms. Found 10 (20 requested) and removed 19 (13 requested) atoms. Cycle 14: After refmac, R = 0.1908 (Rfree = 0.000) for 3519 atoms. Found 9 (19 requested) and removed 20 (13 requested) atoms. Cycle 15: After refmac, R = 0.1810 (Rfree = 0.000) for 3505 atoms. Found 3 (19 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 3600 seeds are put forward NCS extension: 30 residues added (19 deleted due to clashes), 3630 seeds are put forward Round 1: 284 peptides, 35 chains. Longest chain 33 peptides. Score 0.601 Round 2: 320 peptides, 34 chains. Longest chain 45 peptides. Score 0.684 Round 3: 312 peptides, 30 chains. Longest chain 33 peptides. Score 0.703 Round 4: 319 peptides, 28 chains. Longest chain 33 peptides. Score 0.731 Round 5: 314 peptides, 33 chains. Longest chain 36 peptides. Score 0.681 Taking the results from Round 4 Chains 31, Residues 291, Estimated correctness of the model 65.5 % 3 chains (59 residues) have been docked in sequence Building loops using Loopy2018 31 chains (291 residues) following loop building 3 chains (59 residues) in sequence following loop building ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7532 restraints for refining 3688 atoms. 6163 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2290 (Rfree = 0.000) for 3688 atoms. Found 17 (19 requested) and removed 35 (13 requested) atoms. Cycle 17: After refmac, R = 0.2107 (Rfree = 0.000) for 3656 atoms. Found 9 (18 requested) and removed 19 (13 requested) atoms. Cycle 18: After refmac, R = 0.2014 (Rfree = 0.000) for 3638 atoms. Found 5 (18 requested) and removed 19 (13 requested) atoms. Cycle 19: After refmac, R = 0.1954 (Rfree = 0.000) for 3618 atoms. Found 7 (17 requested) and removed 16 (13 requested) atoms. Cycle 20: After refmac, R = 0.1909 (Rfree = 0.000) for 3608 atoms. Found 2 (17 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 3680 seeds are put forward NCS extension: 23 residues added (25 deleted due to clashes), 3703 seeds are put forward Round 1: 286 peptides, 36 chains. Longest chain 18 peptides. Score 0.595 Round 2: 299 peptides, 31 chains. Longest chain 34 peptides. Score 0.671 Round 3: 314 peptides, 31 chains. Longest chain 35 peptides. Score 0.699 Round 4: 302 peptides, 34 chains. Longest chain 36 peptides. Score 0.649 Round 5: 283 peptides, 33 chains. Longest chain 21 peptides. Score 0.619 Taking the results from Round 3 Chains 32, Residues 283, Estimated correctness of the model 57.6 % 3 chains (56 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7628 restraints for refining 3688 atoms. 6308 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2123 (Rfree = 0.000) for 3688 atoms. Found 14 (16 requested) and removed 31 (13 requested) atoms. Cycle 22: After refmac, R = 0.1994 (Rfree = 0.000) for 3659 atoms. Found 7 (16 requested) and removed 15 (13 requested) atoms. Cycle 23: After refmac, R = 0.1902 (Rfree = 0.000) for 3648 atoms. Found 3 (16 requested) and removed 16 (13 requested) atoms. Cycle 24: After refmac, R = 0.1917 (Rfree = 0.000) for 3634 atoms. Found 6 (16 requested) and removed 13 (13 requested) atoms. Cycle 25: After refmac, R = 0.1890 (Rfree = 0.000) for 3627 atoms. Found 0 (16 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.53 Search for helices and strands: 0 residues in 0 chains, 3727 seeds are put forward NCS extension: 20 residues added (15 deleted due to clashes), 3747 seeds are put forward Round 1: 254 peptides, 36 chains. Longest chain 33 peptides. Score 0.518 Round 2: 285 peptides, 31 chains. Longest chain 36 peptides. Score 0.643 Round 3: 291 peptides, 32 chains. Longest chain 32 peptides. Score 0.646 Round 4: 298 peptides, 33 chains. Longest chain 35 peptides. Score 0.650 Round 5: 296 peptides, 33 chains. Longest chain 35 peptides. Score 0.646 Taking the results from Round 4 Chains 33, Residues 265, Estimated correctness of the model 44.1 % 1 chains (34 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 8005 restraints for refining 3687 atoms. 6844 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2217 (Rfree = 0.000) for 3687 atoms. Found 15 (16 requested) and removed 32 (13 requested) atoms. Cycle 27: After refmac, R = 0.2026 (Rfree = 0.000) for 3656 atoms. Found 10 (16 requested) and removed 17 (13 requested) atoms. Cycle 28: After refmac, R = 0.1963 (Rfree = 0.000) for 3641 atoms. Found 4 (16 requested) and removed 13 (13 requested) atoms. Cycle 29: After refmac, R = 0.2059 (Rfree = 0.000) for 3627 atoms. Found 13 (16 requested) and removed 15 (13 requested) atoms. Cycle 30: After refmac, R = 0.1790 (Rfree = 0.000) for 3615 atoms. Found 6 (16 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 3710 seeds are put forward NCS extension: 50 residues added (4 deleted due to clashes), 3760 seeds are put forward Round 1: 238 peptides, 36 chains. Longest chain 17 peptides. Score 0.475 Round 2: 285 peptides, 38 chains. Longest chain 19 peptides. Score 0.572 Round 3: 291 peptides, 37 chains. Longest chain 19 peptides. Score 0.597 Round 4: 296 peptides, 35 chains. Longest chain 33 peptides. Score 0.627 Round 5: 302 peptides, 32 chains. Longest chain 29 peptides. Score 0.667 Taking the results from Round 5 Chains 33, Residues 270, Estimated correctness of the model 49.0 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 8025 restraints for refining 3688 atoms. 6816 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2176 (Rfree = 0.000) for 3688 atoms. Found 16 (16 requested) and removed 23 (13 requested) atoms. Cycle 32: After refmac, R = 0.2037 (Rfree = 0.000) for 3665 atoms. Found 7 (16 requested) and removed 13 (13 requested) atoms. Cycle 33: After refmac, R = 0.2038 (Rfree = 0.000) for 3652 atoms. Found 4 (16 requested) and removed 16 (13 requested) atoms. Cycle 34: After refmac, R = 0.1965 (Rfree = 0.000) for 3636 atoms. Found 5 (16 requested) and removed 18 (13 requested) atoms. Cycle 35: After refmac, R = 0.1944 (Rfree = 0.000) for 3618 atoms. Found 8 (16 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 3708 seeds are put forward NCS extension: 41 residues added (4 deleted due to clashes), 3749 seeds are put forward Round 1: 236 peptides, 42 chains. Longest chain 12 peptides. Score 0.394 Round 2: 266 peptides, 36 chains. Longest chain 18 peptides. Score 0.548 Round 3: 279 peptides, 36 chains. Longest chain 24 peptides. Score 0.579 Round 4: 292 peptides, 37 chains. Longest chain 27 peptides. Score 0.599 Round 5: 280 peptides, 33 chains. Longest chain 36 peptides. Score 0.612 Taking the results from Round 5 Chains 35, Residues 247, Estimated correctness of the model 32.5 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 8007 restraints for refining 3687 atoms. 6926 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2052 (Rfree = 0.000) for 3687 atoms. Found 16 (16 requested) and removed 19 (13 requested) atoms. Cycle 37: After refmac, R = 0.1983 (Rfree = 0.000) for 3673 atoms. Found 12 (16 requested) and removed 15 (13 requested) atoms. Cycle 38: After refmac, R = 0.1947 (Rfree = 0.000) for 3668 atoms. Found 9 (16 requested) and removed 18 (13 requested) atoms. Cycle 39: After refmac, R = 0.1888 (Rfree = 0.000) for 3658 atoms. Found 10 (16 requested) and removed 14 (13 requested) atoms. Cycle 40: After refmac, R = 0.1866 (Rfree = 0.000) for 3652 atoms. Found 7 (16 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 3734 seeds are put forward NCS extension: 61 residues added (13 deleted due to clashes), 3795 seeds are put forward Round 1: 216 peptides, 36 chains. Longest chain 16 peptides. Score 0.411 Round 2: 263 peptides, 38 chains. Longest chain 17 peptides. Score 0.518 Round 3: 244 peptides, 35 chains. Longest chain 17 peptides. Score 0.503 Round 4: 259 peptides, 31 chains. Longest chain 23 peptides. Score 0.585 Round 5: 251 peptides, 34 chains. Longest chain 18 peptides. Score 0.533 Taking the results from Round 4 Chains 33, Residues 228, Estimated correctness of the model 23.7 % 3 chains (45 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7878 restraints for refining 3687 atoms. 6791 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2169 (Rfree = 0.000) for 3687 atoms. Found 16 (16 requested) and removed 37 (13 requested) atoms. Cycle 42: After refmac, R = 0.2047 (Rfree = 0.000) for 3652 atoms. Found 15 (16 requested) and removed 23 (13 requested) atoms. Cycle 43: After refmac, R = 0.1927 (Rfree = 0.000) for 3640 atoms. Found 11 (16 requested) and removed 22 (13 requested) atoms. Cycle 44: After refmac, R = 0.1892 (Rfree = 0.000) for 3624 atoms. Found 12 (16 requested) and removed 14 (13 requested) atoms. Cycle 45: After refmac, R = 0.1800 (Rfree = 0.000) for 3619 atoms. Found 8 (16 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 3725 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3749 seeds are put forward Round 1: 183 peptides, 30 chains. Longest chain 16 peptides. Score 0.391 Round 2: 222 peptides, 32 chains. Longest chain 22 peptides. Score 0.479 Round 3: 217 peptides, 29 chains. Longest chain 22 peptides. Score 0.503 Round 4: 236 peptides, 33 chains. Longest chain 19 peptides. Score 0.505 Round 5: 236 peptides, 32 chains. Longest chain 18 peptides. Score 0.517 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 204, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 1vpm-3_warpNtrace.pdb as input Building loops using Loopy2018 32 chains (204 residues) following loop building 2 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7484 reflections ( 98.11 % complete ) and 8290 restraints for refining 3687 atoms. 7421 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2020 (Rfree = 0.000) for 3687 atoms. Found 0 (16 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1965 (Rfree = 0.000) for 3662 atoms. Found 0 (16 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1901 (Rfree = 0.000) for 3646 atoms. Found 0 (16 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1846 (Rfree = 0.000) for 3631 atoms. Found 0 (16 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:11:14 GMT 2018 Job finished. TimeTaking 44.35 Used memory is bytes: 15025056