Sun 23 Dec 22:23:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vpm-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpm-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpm-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-3.4-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:12 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/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-3.4-parrot-hancs/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-hancs.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-hancs.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 4497 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3076 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2602 (Rfree = 0.000) for 4497 atoms. Found 31 (33 requested) and removed 77 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 4524 seeds are put forward NCS extension: 0 residues added, 4524 seeds are put forward Round 1: 257 peptides, 37 chains. Longest chain 18 peptides. Score 0.514 Round 2: 314 peptides, 37 chains. Longest chain 34 peptides. Score 0.646 Round 3: 332 peptides, 28 chains. Longest chain 36 peptides. Score 0.752 Round 4: 339 peptides, 31 chains. Longest chain 32 peptides. Score 0.740 Round 5: 328 peptides, 32 chains. Longest chain 38 peptides. Score 0.715 Taking the results from Round 3 Chains 35, Residues 304, Estimated correctness of the model 70.3 % 4 chains (57 residues) have been docked in sequence Building loops using Loopy2018 35 chains (304 residues) following loop building 4 chains (57 residues) in sequence following loop building ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7421 restraints for refining 3687 atoms. 6059 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2382 (Rfree = 0.000) for 3687 atoms. Found 20 (27 requested) and removed 63 (13 requested) atoms. Cycle 2: After refmac, R = 0.2317 (Rfree = 0.000) for 3578 atoms. Found 17 (26 requested) and removed 29 (13 requested) atoms. Cycle 3: After refmac, R = 0.2246 (Rfree = 0.000) for 3535 atoms. Found 10 (25 requested) and removed 29 (13 requested) atoms. Cycle 4: After refmac, R = 0.2204 (Rfree = 0.000) for 3499 atoms. Found 10 (24 requested) and removed 25 (13 requested) atoms. Cycle 5: After refmac, R = 0.2134 (Rfree = 0.000) for 3472 atoms. Found 11 (24 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 3609 seeds are put forward NCS extension: 14 residues added (9 deleted due to clashes), 3623 seeds are put forward Round 1: 284 peptides, 40 chains. Longest chain 19 peptides. Score 0.549 Round 2: 327 peptides, 38 chains. Longest chain 45 peptides. Score 0.662 Round 3: 330 peptides, 32 chains. Longest chain 46 peptides. Score 0.718 Round 4: 340 peptides, 30 chains. Longest chain 47 peptides. Score 0.749 Round 5: 352 peptides, 30 chains. Longest chain 40 peptides. Score 0.766 Taking the results from Round 5 Chains 38, Residues 322, Estimated correctness of the model 73.3 % 7 chains (76 residues) have been docked in sequence Building loops using Loopy2018 38 chains (322 residues) following loop building 7 chains (76 residues) in sequence following loop building ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7194 restraints for refining 3683 atoms. 5680 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2518 (Rfree = 0.000) for 3683 atoms. Found 22 (24 requested) and removed 55 (13 requested) atoms. Cycle 7: After refmac, R = 0.2362 (Rfree = 0.000) for 3624 atoms. Found 13 (24 requested) and removed 20 (13 requested) atoms. Cycle 8: After refmac, R = 0.2288 (Rfree = 0.000) for 3598 atoms. Found 15 (23 requested) and removed 39 (13 requested) atoms. Cycle 9: After refmac, R = 0.2233 (Rfree = 0.000) for 3568 atoms. Found 8 (22 requested) and removed 26 (13 requested) atoms. Cycle 10: After refmac, R = 0.2156 (Rfree = 0.000) for 3541 atoms. Found 12 (21 requested) and removed 28 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 3619 seeds are put forward NCS extension: 34 residues added (18 deleted due to clashes), 3653 seeds are put forward Round 1: 304 peptides, 39 chains. Longest chain 19 peptides. Score 0.605 Round 2: 316 peptides, 32 chains. Longest chain 40 peptides. Score 0.694 Round 3: 331 peptides, 28 chains. Longest chain 30 peptides. Score 0.750 Round 4: 345 peptides, 32 chains. Longest chain 39 peptides. Score 0.742 Round 5: 343 peptides, 30 chains. Longest chain 43 peptides. Score 0.753 Taking the results from Round 5 Chains 33, Residues 313, Estimated correctness of the model 70.5 % 3 chains (63 residues) have been docked in sequence Building loops using Loopy2018 33 chains (313 residues) following loop building 3 chains (63 residues) in sequence following loop building ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7241 restraints for refining 3688 atoms. 5803 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2488 (Rfree = 0.000) for 3688 atoms. Found 17 (22 requested) and removed 71 (13 requested) atoms. Cycle 12: After refmac, R = 0.2352 (Rfree = 0.000) for 3613 atoms. Found 18 (21 requested) and removed 27 (13 requested) atoms. Cycle 13: After refmac, R = 0.2308 (Rfree = 0.000) for 3588 atoms. Found 16 (21 requested) and removed 23 (13 requested) atoms. Cycle 14: After refmac, R = 0.2219 (Rfree = 0.000) for 3571 atoms. Found 19 (20 requested) and removed 22 (13 requested) atoms. Cycle 15: After refmac, R = 0.2208 (Rfree = 0.000) for 3557 atoms. Found 9 (19 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 3678 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 3690 seeds are put forward Round 1: 279 peptides, 34 chains. Longest chain 17 peptides. Score 0.600 Round 2: 300 peptides, 31 chains. Longest chain 32 peptides. Score 0.673 Round 3: 309 peptides, 36 chains. Longest chain 22 peptides. Score 0.645 Round 4: 311 peptides, 31 chains. Longest chain 21 peptides. Score 0.693 Round 5: 319 peptides, 36 chains. Longest chain 27 peptides. Score 0.665 Taking the results from Round 4 Chains 36, Residues 280, Estimated correctness of the model 56.1 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7608 restraints for refining 3688 atoms. 6343 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2513 (Rfree = 0.000) for 3688 atoms. Found 15 (19 requested) and removed 34 (13 requested) atoms. Cycle 17: After refmac, R = 0.2437 (Rfree = 0.000) for 3659 atoms. Found 19 (19 requested) and removed 24 (13 requested) atoms. Cycle 18: After refmac, R = 0.2333 (Rfree = 0.000) for 3646 atoms. Found 8 (19 requested) and removed 20 (13 requested) atoms. Cycle 19: After refmac, R = 0.2292 (Rfree = 0.000) for 3626 atoms. Found 10 (19 requested) and removed 26 (13 requested) atoms. Cycle 20: After refmac, R = 0.2194 (Rfree = 0.000) for 3607 atoms. Found 10 (19 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 3728 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3749 seeds are put forward Round 1: 245 peptides, 31 chains. Longest chain 27 peptides. Score 0.552 Round 2: 275 peptides, 28 chains. Longest chain 29 peptides. Score 0.651 Round 3: 283 peptides, 26 chains. Longest chain 32 peptides. Score 0.685 Round 4: 281 peptides, 28 chains. Longest chain 29 peptides. Score 0.663 Round 5: 279 peptides, 27 chains. Longest chain 24 peptides. Score 0.668 Taking the results from Round 3 Chains 28, Residues 257, Estimated correctness of the model 53.9 % 2 chains (48 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7832 restraints for refining 3688 atoms. 6630 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2338 (Rfree = 0.000) for 3688 atoms. Found 12 (19 requested) and removed 31 (13 requested) atoms. Cycle 22: After refmac, R = 0.2234 (Rfree = 0.000) for 3659 atoms. Found 13 (19 requested) and removed 22 (13 requested) atoms. Cycle 23: After refmac, R = 0.2148 (Rfree = 0.000) for 3642 atoms. Found 16 (19 requested) and removed 20 (13 requested) atoms. Cycle 24: After refmac, R = 0.2091 (Rfree = 0.000) for 3631 atoms. Found 13 (19 requested) and removed 19 (13 requested) atoms. Cycle 25: After refmac, R = 0.2092 (Rfree = 0.000) for 3620 atoms. Found 10 (19 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 3718 seeds are put forward NCS extension: 36 residues added (12 deleted due to clashes), 3754 seeds are put forward Round 1: 242 peptides, 34 chains. Longest chain 21 peptides. Score 0.509 Round 2: 280 peptides, 30 chains. Longest chain 26 peptides. Score 0.642 Round 3: 271 peptides, 31 chains. Longest chain 21 peptides. Score 0.613 Round 4: 257 peptides, 33 chains. Longest chain 18 peptides. Score 0.559 Round 5: 258 peptides, 27 chains. Longest chain 21 peptides. Score 0.625 Taking the results from Round 2 Chains 31, Residues 250, Estimated correctness of the model 41.8 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 7862 restraints for refining 3688 atoms. 6740 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2165 (Rfree = 0.000) for 3688 atoms. Found 18 (19 requested) and removed 42 (13 requested) atoms. Cycle 27: After refmac, R = 0.2065 (Rfree = 0.000) for 3659 atoms. Found 9 (19 requested) and removed 30 (13 requested) atoms. Cycle 28: After refmac, R = 0.2053 (Rfree = 0.000) for 3635 atoms. Found 13 (19 requested) and removed 17 (13 requested) atoms. Cycle 29: After refmac, R = 0.1996 (Rfree = 0.000) for 3628 atoms. Found 14 (19 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.1951 (Rfree = 0.000) for 3625 atoms. Found 12 (19 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 3731 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 3758 seeds are put forward Round 1: 241 peptides, 33 chains. Longest chain 16 peptides. Score 0.518 Round 2: 262 peptides, 29 chains. Longest chain 24 peptides. Score 0.613 Round 3: 267 peptides, 31 chains. Longest chain 24 peptides. Score 0.604 Round 4: 279 peptides, 32 chains. Longest chain 20 peptides. Score 0.620 Round 5: 271 peptides, 29 chains. Longest chain 24 peptides. Score 0.633 Taking the results from Round 5 Chains 29, Residues 242, Estimated correctness of the model 39.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 8446 restraints for refining 3688 atoms. 7507 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2207 (Rfree = 0.000) for 3688 atoms. Found 19 (19 requested) and removed 21 (13 requested) atoms. Cycle 32: After refmac, R = 0.2067 (Rfree = 0.000) for 3680 atoms. Found 9 (19 requested) and removed 17 (13 requested) atoms. Cycle 33: After refmac, R = 0.2103 (Rfree = 0.000) for 3664 atoms. Found 17 (19 requested) and removed 19 (13 requested) atoms. Cycle 34: After refmac, R = 0.2007 (Rfree = 0.000) for 3656 atoms. Found 16 (19 requested) and removed 18 (13 requested) atoms. Cycle 35: After refmac, R = 0.2014 (Rfree = 0.000) for 3647 atoms. Found 7 (19 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 3755 seeds are put forward NCS extension: 23 residues added (15 deleted due to clashes), 3778 seeds are put forward Round 1: 237 peptides, 37 chains. Longest chain 14 peptides. Score 0.460 Round 2: 277 peptides, 32 chains. Longest chain 21 peptides. Score 0.616 Round 3: 277 peptides, 33 chains. Longest chain 21 peptides. Score 0.606 Round 4: 278 peptides, 33 chains. Longest chain 16 peptides. Score 0.608 Round 5: 282 peptides, 35 chains. Longest chain 20 peptides. Score 0.597 Taking the results from Round 2 Chains 34, Residues 245, Estimated correctness of the model 33.8 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7484 reflections ( 98.11 % complete ) and 8060 restraints for refining 3687 atoms. 7015 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2140 (Rfree = 0.000) for 3687 atoms. Found 11 (19 requested) and removed 14 (13 requested) atoms. Cycle 37: After refmac, R = 0.2178 (Rfree = 0.000) for 3674 atoms. Found 8 (19 requested) and removed 15 (13 requested) atoms. Cycle 38: After refmac, R = 0.2107 (Rfree = 0.000) for 3659 atoms. Found 9 (19 requested) and removed 17 (13 requested) atoms. Cycle 39: After refmac, R = 0.2100 (Rfree = 0.000) for 3646 atoms. Found 10 (19 requested) and removed 17 (13 requested) atoms. Cycle 40: After refmac, R = 0.2031 (Rfree = 0.000) for 3637 atoms. Found 9 (19 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 3721 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3733 seeds are put forward Round 1: 216 peptides, 32 chains. Longest chain 14 peptides. Score 0.462 Round 2: 238 peptides, 28 chains. Longest chain 23 peptides. Score 0.568 Round 3: 247 peptides, 30 chains. Longest chain 27 peptides. Score 0.568 Round 4: 252 peptides, 30 chains. Longest chain 16 peptides. Score 0.580 Round 5: 253 peptides, 28 chains. Longest chain 35 peptides. Score 0.604 Taking the results from Round 5 Chains 30, Residues 225, Estimated correctness of the model 30.0 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7484 reflections ( 98.11 % complete ) and 8168 restraints for refining 3688 atoms. 7183 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2224 (Rfree = 0.000) for 3688 atoms. Found 19 (19 requested) and removed 26 (13 requested) atoms. Cycle 42: After refmac, R = 0.2123 (Rfree = 0.000) for 3678 atoms. Found 14 (19 requested) and removed 20 (13 requested) atoms. Cycle 43: After refmac, R = 0.2118 (Rfree = 0.000) for 3670 atoms. Found 14 (19 requested) and removed 20 (13 requested) atoms. Cycle 44: After refmac, R = 0.2055 (Rfree = 0.000) for 3661 atoms. Found 19 (19 requested) and removed 21 (13 requested) atoms. Cycle 45: After refmac, R = 0.1773 (Rfree = 0.000) for 3650 atoms. Found 4 (19 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 3743 seeds are put forward NCS extension: 19 residues added (8 deleted due to clashes), 3762 seeds are put forward Round 1: 207 peptides, 32 chains. Longest chain 15 peptides. Score 0.437 Round 2: 257 peptides, 35 chains. Longest chain 24 peptides. Score 0.537 Round 3: 237 peptides, 32 chains. Longest chain 19 peptides. Score 0.520 Round 4: 230 peptides, 33 chains. Longest chain 16 peptides. Score 0.489 Round 5: 246 peptides, 33 chains. Longest chain 20 peptides. Score 0.531 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 222, Estimated correctness of the model 6.8 % 1 chains (23 residues) have been docked in sequence Sequence coverage is 10 % 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 8257 restraints for refining 3687 atoms. 7308 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2058 (Rfree = 0.000) for 3687 atoms. Found 0 (19 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2032 (Rfree = 0.000) for 3666 atoms. Found 0 (19 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2081 (Rfree = 0.000) for 3650 atoms. Found 0 (19 requested) and removed 10 (13 requested) atoms. Cycle 49: After refmac, R = 0.1946 (Rfree = 0.000) for 3635 atoms. TimeTaking 61.68