null Mon 24 Dec 07:28:54 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vpm-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vpm-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.6-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 07:28:59 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/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.6-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 338 and 0 Target number of residues in the AU: 338 Target solvent content: 0.6553 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 81.12 6312 reflections ( 97.92 % complete ) and 0 restraints for refining 4486 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3186 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2908 (Rfree = 0.000) for 4486 atoms. Found 28 (28 requested) and removed 49 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 4538 seeds are put forward NCS extension: 0 residues added, 4538 seeds are put forward Round 1: 226 peptides, 40 chains. Longest chain 16 peptides. Score 0.389 Round 2: 283 peptides, 34 chains. Longest chain 18 peptides. Score 0.609 Round 3: 299 peptides, 37 chains. Longest chain 23 peptides. Score 0.614 Round 4: 326 peptides, 38 chains. Longest chain 19 peptides. Score 0.660 Round 5: 317 peptides, 36 chains. Longest chain 27 peptides. Score 0.661 Taking the results from Round 5 Chains 38, Residues 281, Estimated correctness of the model 37.0 % 5 chains (69 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 7497 restraints for refining 3675 atoms. 6123 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2434 (Rfree = 0.000) for 3675 atoms. Found 22 (23 requested) and removed 51 (11 requested) atoms. Cycle 2: After refmac, R = 0.2237 (Rfree = 0.000) for 3572 atoms. Found 17 (23 requested) and removed 30 (11 requested) atoms. Cycle 3: After refmac, R = 0.2151 (Rfree = 0.000) for 3527 atoms. Found 14 (22 requested) and removed 15 (11 requested) atoms. Cycle 4: After refmac, R = 0.2079 (Rfree = 0.000) for 3511 atoms. Found 5 (22 requested) and removed 22 (11 requested) atoms. Cycle 5: After refmac, R = 0.2063 (Rfree = 0.000) for 3488 atoms. Found 5 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 3582 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 3614 seeds are put forward Round 1: 264 peptides, 38 chains. Longest chain 15 peptides. Score 0.521 Round 2: 308 peptides, 34 chains. Longest chain 22 peptides. Score 0.661 Round 3: 314 peptides, 33 chains. Longest chain 22 peptides. Score 0.681 Round 4: 304 peptides, 29 chains. Longest chain 25 peptides. Score 0.698 Round 5: 302 peptides, 35 chains. Longest chain 35 peptides. Score 0.640 Taking the results from Round 4 Chains 32, Residues 275, Estimated correctness of the model 49.0 % 4 chains (61 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 7536 restraints for refining 3665 atoms. 6210 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2494 (Rfree = 0.000) for 3665 atoms. Found 21 (23 requested) and removed 64 (11 requested) atoms. Cycle 7: After refmac, R = 0.2304 (Rfree = 0.000) for 3595 atoms. Found 12 (23 requested) and removed 30 (11 requested) atoms. Cycle 8: After refmac, R = 0.2225 (Rfree = 0.000) for 3569 atoms. Found 7 (22 requested) and removed 22 (11 requested) atoms. Cycle 9: After refmac, R = 0.2156 (Rfree = 0.000) for 3550 atoms. Found 3 (22 requested) and removed 14 (11 requested) atoms. Cycle 10: After refmac, R = 0.2137 (Rfree = 0.000) for 3536 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 3633 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3649 seeds are put forward Round 1: 280 peptides, 42 chains. Longest chain 18 peptides. Score 0.516 Round 2: 311 peptides, 34 chains. Longest chain 20 peptides. Score 0.667 Round 3: 293 peptides, 35 chains. Longest chain 25 peptides. Score 0.621 Round 4: 303 peptides, 34 chains. Longest chain 30 peptides. Score 0.651 Round 5: 307 peptides, 38 chains. Longest chain 19 peptides. Score 0.622 Taking the results from Round 2 Chains 38, Residues 277, Estimated correctness of the model 39.0 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 7732 restraints for refining 3638 atoms. 6504 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2331 (Rfree = 0.000) for 3638 atoms. Found 14 (23 requested) and removed 38 (11 requested) atoms. Cycle 12: After refmac, R = 0.2214 (Rfree = 0.000) for 3596 atoms. Found 4 (23 requested) and removed 23 (11 requested) atoms. Cycle 13: After refmac, R = 0.2182 (Rfree = 0.000) for 3575 atoms. Found 4 (22 requested) and removed 16 (11 requested) atoms. Cycle 14: After refmac, R = 0.2180 (Rfree = 0.000) for 3559 atoms. Found 6 (22 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.2108 (Rfree = 0.000) for 3550 atoms. Found 3 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 3653 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3675 seeds are put forward Round 1: 257 peptides, 39 chains. Longest chain 12 peptides. Score 0.490 Round 2: 277 peptides, 35 chains. Longest chain 18 peptides. Score 0.585 Round 3: 294 peptides, 39 chains. Longest chain 17 peptides. Score 0.583 Round 4: 269 peptides, 35 chains. Longest chain 17 peptides. Score 0.566 Round 5: 290 peptides, 34 chains. Longest chain 24 peptides. Score 0.624 Taking the results from Round 5 Chains 36, Residues 256, Estimated correctness of the model 23.8 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8283 restraints for refining 3676 atoms. 7216 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2450 (Rfree = 0.000) for 3676 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Cycle 17: After refmac, R = 0.2279 (Rfree = 0.000) for 3665 atoms. Found 7 (23 requested) and removed 14 (11 requested) atoms. Cycle 18: After refmac, R = 0.2239 (Rfree = 0.000) for 3649 atoms. Found 6 (23 requested) and removed 12 (11 requested) atoms. Cycle 19: After refmac, R = 0.2168 (Rfree = 0.000) for 3638 atoms. Found 5 (23 requested) and removed 14 (11 requested) atoms. Cycle 20: After refmac, R = 0.2339 (Rfree = 0.000) for 3613 atoms. Found 15 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 3.58 Search for helices and strands: 0 residues in 0 chains, 3720 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3739 seeds are put forward Round 1: 243 peptides, 43 chains. Longest chain 11 peptides. Score 0.402 Round 2: 275 peptides, 38 chains. Longest chain 22 peptides. Score 0.548 Round 3: 281 peptides, 41 chains. Longest chain 15 peptides. Score 0.530 Round 4: 266 peptides, 38 chains. Longest chain 12 peptides. Score 0.526 Round 5: 281 peptides, 35 chains. Longest chain 22 peptides. Score 0.594 Taking the results from Round 5 Chains 37, Residues 246, Estimated correctness of the model 12.3 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8425 restraints for refining 3677 atoms. 7442 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2087 (Rfree = 0.000) for 3677 atoms. Found 21 (23 requested) and removed 18 (11 requested) atoms. Cycle 22: After refmac, R = 0.1899 (Rfree = 0.000) for 3665 atoms. Found 4 (23 requested) and removed 13 (11 requested) atoms. Cycle 23: After refmac, R = 0.1833 (Rfree = 0.000) for 3654 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.1807 (Rfree = 0.000) for 3640 atoms. Found 8 (23 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.1733 (Rfree = 0.000) for 3636 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 3734 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3759 seeds are put forward Round 1: 230 peptides, 39 chains. Longest chain 13 peptides. Score 0.414 Round 2: 252 peptides, 35 chains. Longest chain 14 peptides. Score 0.524 Round 3: 262 peptides, 35 chains. Longest chain 14 peptides. Score 0.549 Round 4: 259 peptides, 31 chains. Longest chain 18 peptides. Score 0.585 Round 5: 253 peptides, 38 chains. Longest chain 14 peptides. Score 0.492 Taking the results from Round 4 Chains 32, Residues 228, Estimated correctness of the model 8.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8533 restraints for refining 3677 atoms. 7626 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2058 (Rfree = 0.000) for 3677 atoms. Found 17 (23 requested) and removed 15 (11 requested) atoms. Cycle 27: After refmac, R = 0.1898 (Rfree = 0.000) for 3663 atoms. Found 15 (23 requested) and removed 17 (11 requested) atoms. Cycle 28: After refmac, R = 0.1805 (Rfree = 0.000) for 3655 atoms. Found 16 (23 requested) and removed 14 (11 requested) atoms. Cycle 29: After refmac, R = 0.1741 (Rfree = 0.000) for 3652 atoms. Found 15 (23 requested) and removed 18 (11 requested) atoms. Cycle 30: After refmac, R = 0.1779 (Rfree = 0.000) for 3645 atoms. Found 15 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 3763 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 3782 seeds are put forward Round 1: 209 peptides, 38 chains. Longest chain 11 peptides. Score 0.363 Round 2: 242 peptides, 38 chains. Longest chain 15 peptides. Score 0.461 Round 3: 253 peptides, 37 chains. Longest chain 15 peptides. Score 0.503 Round 4: 263 peptides, 38 chains. Longest chain 18 peptides. Score 0.518 Round 5: 265 peptides, 38 chains. Longest chain 15 peptides. Score 0.523 Taking the results from Round 5 Chains 38, Residues 227, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8569 restraints for refining 3676 atoms. 7699 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1869 (Rfree = 0.000) for 3676 atoms. Found 12 (23 requested) and removed 27 (11 requested) atoms. Cycle 32: After refmac, R = 0.1748 (Rfree = 0.000) for 3645 atoms. Found 7 (23 requested) and removed 16 (11 requested) atoms. Cycle 33: After refmac, R = 0.1688 (Rfree = 0.000) for 3631 atoms. Found 6 (23 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.1643 (Rfree = 0.000) for 3620 atoms. Found 7 (23 requested) and removed 18 (11 requested) atoms. Cycle 35: After refmac, R = 0.1584 (Rfree = 0.000) for 3606 atoms. Found 5 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 3714 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3735 seeds are put forward Round 1: 201 peptides, 39 chains. Longest chain 10 peptides. Score 0.324 Round 2: 230 peptides, 38 chains. Longest chain 13 peptides. Score 0.427 Round 3: 222 peptides, 36 chains. Longest chain 13 peptides. Score 0.429 Round 4: 242 peptides, 35 chains. Longest chain 15 peptides. Score 0.498 Round 5: 240 peptides, 37 chains. Longest chain 14 peptides. Score 0.468 Taking the results from Round 4 Chains 35, Residues 207, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8479 restraints for refining 3676 atoms. 7642 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1792 (Rfree = 0.000) for 3676 atoms. Found 10 (23 requested) and removed 20 (11 requested) atoms. Cycle 37: After refmac, R = 0.1610 (Rfree = 0.000) for 3652 atoms. Found 5 (23 requested) and removed 14 (11 requested) atoms. Cycle 38: After refmac, R = 0.1572 (Rfree = 0.000) for 3637 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.1579 (Rfree = 0.000) for 3623 atoms. Found 2 (23 requested) and removed 19 (11 requested) atoms. Cycle 40: After refmac, R = 0.1581 (Rfree = 0.000) for 3603 atoms. Found 7 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 3700 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3718 seeds are put forward Round 1: 196 peptides, 39 chains. Longest chain 12 peptides. Score 0.308 Round 2: 223 peptides, 37 chains. Longest chain 12 peptides. Score 0.419 Round 3: 227 peptides, 35 chains. Longest chain 16 peptides. Score 0.456 Round 4: 215 peptides, 33 chains. Longest chain 13 peptides. Score 0.447 Round 5: 227 peptides, 32 chains. Longest chain 13 peptides. Score 0.493 Taking the results from Round 5 Chains 32, Residues 195, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8439 restraints for refining 3677 atoms. 7621 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1940 (Rfree = 0.000) for 3677 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 42: After refmac, R = 0.1774 (Rfree = 0.000) for 3662 atoms. Found 8 (23 requested) and removed 16 (11 requested) atoms. Cycle 43: After refmac, R = 0.1798 (Rfree = 0.000) for 3647 atoms. Found 11 (23 requested) and removed 20 (11 requested) atoms. Cycle 44: After refmac, R = 0.1747 (Rfree = 0.000) for 3635 atoms. Found 7 (23 requested) and removed 15 (11 requested) atoms. Cycle 45: After refmac, R = 0.1727 (Rfree = 0.000) for 3624 atoms. Found 2 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 3709 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 3720 seeds are put forward Round 1: 202 peptides, 38 chains. Longest chain 13 peptides. Score 0.341 Round 2: 219 peptides, 36 chains. Longest chain 14 peptides. Score 0.420 Round 3: 225 peptides, 35 chains. Longest chain 12 peptides. Score 0.450 Round 4: 238 peptides, 35 chains. Longest chain 18 peptides. Score 0.487 Round 5: 233 peptides, 35 chains. Longest chain 21 peptides. Score 0.473 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 203, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vpm-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6312 reflections ( 97.92 % complete ) and 8493 restraints for refining 3676 atoms. 7676 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1912 (Rfree = 0.000) for 3676 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1854 (Rfree = 0.000) for 3652 atoms. Found 0 (23 requested) and removed 10 (11 requested) atoms. Cycle 48: After refmac, R = 0.1820 (Rfree = 0.000) for 3638 atoms. Found 0 (23 requested) and removed 8 (11 requested) atoms. Cycle 49: After refmac, R = 0.1781 (Rfree = 0.000) for 3630 atoms. Found 0 (23 requested) and removed 0 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:15:05 GMT 2018 Job finished. TimeTaking 46.18 Used memory is bytes: 16538072