Mon 24 Dec 01:01:36 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vpm-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vpm-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.6-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 01:01:41 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-3.6-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 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-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-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4056 target number of atoms Had to go as low as 0.60 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 Failed to save intermediate PDB 6312 reflections ( 97.92 % complete ) and 0 restraints for refining 4504 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3120 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2907 (Rfree = 0.000) for 4504 atoms. Found 28 (28 requested) and removed 95 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 4523 seeds are put forward NCS extension: 0 residues added, 4523 seeds are put forward Round 1: 236 peptides, 41 chains. Longest chain 17 peptides. Score 0.407 Round 2: 294 peptides, 42 chains. Longest chain 16 peptides. Score 0.551 Round 3: 334 peptides, 38 chains. Longest chain 30 peptides. Score 0.676 Round 4: 325 peptides, 34 chains. Longest chain 27 peptides. Score 0.693 Round 5: 335 peptides, 35 chains. Longest chain 23 peptides. Score 0.702 Taking the results from Round 5 Chains 41, Residues 300, Estimated correctness of the model 50.2 % 4 chains (54 residues) have been docked in sequence Building loops using Loopy2018 41 chains (300 residues) following loop building 4 chains (54 residues) in sequence following loop building ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 7686 restraints for refining 3674 atoms. 6343 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2490 (Rfree = 0.000) for 3674 atoms. Found 18 (23 requested) and removed 39 (11 requested) atoms. Cycle 2: After refmac, R = 0.2362 (Rfree = 0.000) for 3564 atoms. Found 19 (23 requested) and removed 31 (11 requested) atoms. Cycle 3: After refmac, R = 0.2291 (Rfree = 0.000) for 3522 atoms. Found 11 (21 requested) and removed 17 (11 requested) atoms. Cycle 4: After refmac, R = 0.2208 (Rfree = 0.000) for 3504 atoms. Found 8 (21 requested) and removed 24 (11 requested) atoms. Cycle 5: After refmac, R = 0.2192 (Rfree = 0.000) for 3484 atoms. Found 4 (20 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 3598 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 3614 seeds are put forward Round 1: 284 peptides, 43 chains. Longest chain 19 peptides. Score 0.516 Round 2: 306 peptides, 38 chains. Longest chain 22 peptides. Score 0.620 Round 3: 302 peptides, 40 chains. Longest chain 19 peptides. Score 0.591 Round 4: 301 peptides, 38 chains. Longest chain 26 peptides. Score 0.609 Round 5: 303 peptides, 35 chains. Longest chain 19 peptides. Score 0.642 Taking the results from Round 5 Chains 37, Residues 268, Estimated correctness of the model 30.3 % 6 chains (41 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 7737 restraints for refining 3561 atoms. 6591 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2416 (Rfree = 0.000) for 3561 atoms. Found 17 (20 requested) and removed 47 (11 requested) atoms. Cycle 7: After refmac, R = 0.2185 (Rfree = 0.000) for 3519 atoms. Found 10 (20 requested) and removed 24 (11 requested) atoms. Cycle 8: After refmac, R = 0.2140 (Rfree = 0.000) for 3499 atoms. Found 4 (20 requested) and removed 20 (11 requested) atoms. Cycle 9: After refmac, R = 0.2084 (Rfree = 0.000) for 3480 atoms. Found 2 (20 requested) and removed 12 (11 requested) atoms. Cycle 10: After refmac, R = 0.2060 (Rfree = 0.000) for 3466 atoms. Found 5 (20 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 3556 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 3574 seeds are put forward Round 1: 265 peptides, 38 chains. Longest chain 16 peptides. Score 0.523 Round 2: 306 peptides, 38 chains. Longest chain 22 peptides. Score 0.620 Round 3: 295 peptides, 34 chains. Longest chain 25 peptides. Score 0.635 Round 4: 304 peptides, 35 chains. Longest chain 24 peptides. Score 0.644 Round 5: 300 peptides, 35 chains. Longest chain 26 peptides. Score 0.636 Taking the results from Round 4 Chains 36, Residues 269, Estimated correctness of the model 31.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8025 restraints for refining 3639 atoms. 6890 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2117 (Rfree = 0.000) for 3639 atoms. Found 13 (21 requested) and removed 83 (11 requested) atoms. Cycle 12: After refmac, R = 0.1998 (Rfree = 0.000) for 3562 atoms. Found 9 (20 requested) and removed 44 (11 requested) atoms. Cycle 13: After refmac, R = 0.1951 (Rfree = 0.000) for 3523 atoms. Found 8 (20 requested) and removed 32 (11 requested) atoms. Cycle 14: After refmac, R = 0.2076 (Rfree = 0.000) for 3485 atoms. Found 11 (20 requested) and removed 33 (11 requested) atoms. Cycle 15: After refmac, R = 0.1866 (Rfree = 0.000) for 3453 atoms. Found 12 (20 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 3595 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3619 seeds are put forward Round 1: 257 peptides, 42 chains. Longest chain 12 peptides. Score 0.455 Round 2: 275 peptides, 33 chains. Longest chain 21 peptides. Score 0.601 Round 3: 295 peptides, 33 chains. Longest chain 34 peptides. Score 0.644 Round 4: 288 peptides, 32 chains. Longest chain 25 peptides. Score 0.639 Round 5: 288 peptides, 35 chains. Longest chain 28 peptides. Score 0.610 Taking the results from Round 3 Chains 33, Residues 262, Estimated correctness of the model 31.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8159 restraints for refining 3595 atoms. 7144 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2020 (Rfree = 0.000) for 3595 atoms. Found 20 (21 requested) and removed 38 (11 requested) atoms. Cycle 17: After refmac, R = 0.1841 (Rfree = 0.000) for 3569 atoms. Found 7 (20 requested) and removed 15 (11 requested) atoms. Cycle 18: After refmac, R = 0.1804 (Rfree = 0.000) for 3555 atoms. Found 3 (20 requested) and removed 17 (11 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1761 (Rfree = 0.000) for 3541 atoms. Found 1 (20 requested) and removed 14 (11 requested) atoms. Cycle 20: After refmac, R = 0.1767 (Rfree = 0.000) for 3528 atoms. Found 2 (20 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 3597 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 3630 seeds are put forward Round 1: 241 peptides, 42 chains. Longest chain 11 peptides. Score 0.409 Round 2: 270 peptides, 37 chains. Longest chain 25 peptides. Score 0.547 Round 3: 293 peptides, 37 chains. Longest chain 20 peptides. Score 0.601 Round 4: 280 peptides, 36 chains. Longest chain 25 peptides. Score 0.582 Round 5: 282 peptides, 37 chains. Longest chain 21 peptides. Score 0.576 Taking the results from Round 3 Chains 37, Residues 256, Estimated correctness of the model 15.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8100 restraints for refining 3658 atoms. 7048 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2035 (Rfree = 0.000) for 3658 atoms. Found 20 (21 requested) and removed 55 (11 requested) atoms. Cycle 22: After refmac, R = 0.1808 (Rfree = 0.000) for 3618 atoms. Found 6 (21 requested) and removed 21 (11 requested) atoms. Cycle 23: After refmac, R = 0.1784 (Rfree = 0.000) for 3600 atoms. Found 4 (21 requested) and removed 21 (11 requested) atoms. Cycle 24: After refmac, R = 0.1746 (Rfree = 0.000) for 3578 atoms. Found 7 (20 requested) and removed 13 (11 requested) atoms. Cycle 25: After refmac, R = 0.1706 (Rfree = 0.000) for 3571 atoms. Found 2 (20 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 3671 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3693 seeds are put forward Round 1: 234 peptides, 41 chains. Longest chain 12 peptides. Score 0.401 Round 2: 269 peptides, 40 chains. Longest chain 19 peptides. Score 0.511 Round 3: 250 peptides, 38 chains. Longest chain 11 peptides. Score 0.483 Round 4: 264 peptides, 41 chains. Longest chain 12 peptides. Score 0.486 Round 5: 272 peptides, 38 chains. Longest chain 21 peptides. Score 0.541 Taking the results from Round 5 Chains 39, Residues 234, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8464 restraints for refining 3677 atoms. 7537 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1932 (Rfree = 0.000) for 3677 atoms. Found 19 (21 requested) and removed 24 (11 requested) atoms. Cycle 27: After refmac, R = 0.1759 (Rfree = 0.000) for 3653 atoms. Found 7 (21 requested) and removed 14 (11 requested) atoms. Cycle 28: After refmac, R = 0.1724 (Rfree = 0.000) for 3644 atoms. Found 5 (21 requested) and removed 15 (11 requested) atoms. Cycle 29: After refmac, R = 0.1710 (Rfree = 0.000) for 3631 atoms. Found 4 (21 requested) and removed 12 (11 requested) atoms. Cycle 30: After refmac, R = 0.1688 (Rfree = 0.000) for 3621 atoms. Found 1 (21 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 3721 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3742 seeds are put forward Round 1: 216 peptides, 42 chains. Longest chain 11 peptides. Score 0.332 Round 2: 250 peptides, 39 chains. Longest chain 15 peptides. Score 0.471 Round 3: 257 peptides, 41 chains. Longest chain 16 peptides. Score 0.467 Round 4: 247 peptides, 35 chains. Longest chain 17 peptides. Score 0.511 Round 5: 246 peptides, 34 chains. Longest chain 17 peptides. Score 0.520 Taking the results from Round 5 Chains 34, Residues 212, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8573 restraints for refining 3677 atoms. 7741 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2085 (Rfree = 0.000) for 3677 atoms. Found 18 (21 requested) and removed 16 (11 requested) atoms. Cycle 32: After refmac, R = 0.1851 (Rfree = 0.000) for 3668 atoms. Found 7 (21 requested) and removed 14 (11 requested) atoms. Cycle 33: After refmac, R = 0.1772 (Rfree = 0.000) for 3656 atoms. Found 4 (21 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.1729 (Rfree = 0.000) for 3643 atoms. Found 5 (21 requested) and removed 12 (11 requested) atoms. Cycle 35: After refmac, R = 0.1712 (Rfree = 0.000) for 3632 atoms. Found 2 (21 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 3739 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3759 seeds are put forward Round 1: 202 peptides, 37 chains. Longest chain 10 peptides. Score 0.355 Round 2: 216 peptides, 35 chains. Longest chain 15 peptides. Score 0.424 Round 3: 236 peptides, 34 chains. Longest chain 18 peptides. Score 0.493 Round 4: 231 peptides, 34 chains. Longest chain 14 peptides. Score 0.480 Round 5: 231 peptides, 34 chains. Longest chain 18 peptides. Score 0.480 Taking the results from Round 3 Chains 34, Residues 202, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8525 restraints for refining 3676 atoms. 7751 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1940 (Rfree = 0.000) for 3676 atoms. Found 14 (21 requested) and removed 26 (11 requested) atoms. Cycle 37: After refmac, R = 0.1833 (Rfree = 0.000) for 3647 atoms. Found 9 (21 requested) and removed 24 (11 requested) atoms. Cycle 38: After refmac, R = 0.2040 (Rfree = 0.000) for 3630 atoms. Found 12 (21 requested) and removed 14 (11 requested) atoms. Cycle 39: After refmac, R = 0.1882 (Rfree = 0.000) for 3618 atoms. Found 19 (21 requested) and removed 19 (11 requested) atoms. Cycle 40: After refmac, R = 0.1607 (Rfree = 0.000) for 3606 atoms. Found 10 (21 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 3725 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3746 seeds are put forward Round 1: 206 peptides, 42 chains. Longest chain 10 peptides. Score 0.299 Round 2: 209 peptides, 37 chains. Longest chain 16 peptides. Score 0.377 Round 3: 212 peptides, 36 chains. Longest chain 11 peptides. Score 0.399 Round 4: 210 peptides, 33 chains. Longest chain 16 peptides. Score 0.432 Round 5: 213 peptides, 36 chains. Longest chain 13 peptides. Score 0.402 Taking the results from Round 4 Chains 34, Residues 177, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6312 reflections ( 97.92 % complete ) and 8596 restraints for refining 3668 atoms. 7883 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1889 (Rfree = 0.000) for 3668 atoms. Found 21 (21 requested) and removed 15 (11 requested) atoms. Cycle 42: After refmac, R = 0.1686 (Rfree = 0.000) for 3664 atoms. Found 10 (21 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.1660 (Rfree = 0.000) for 3658 atoms. Found 6 (21 requested) and removed 14 (11 requested) atoms. Cycle 44: After refmac, R = 0.1646 (Rfree = 0.000) for 3650 atoms. Found 7 (21 requested) and removed 14 (11 requested) atoms. Cycle 45: After refmac, R = 0.1828 (Rfree = 0.000) for 3640 atoms. Found 21 (21 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 3745 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3759 seeds are put forward Round 1: 187 peptides, 39 chains. Longest chain 10 peptides. Score 0.278 Round 2: 226 peptides, 36 chains. Longest chain 21 peptides. Score 0.441 Round 3: 242 peptides, 38 chains. Longest chain 22 peptides. Score 0.461 Round 4: 224 peptides, 34 chains. Longest chain 20 peptides. Score 0.460 Round 5: 231 peptides, 35 chains. Longest chain 16 peptides. Score 0.467 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 196, Estimated correctness of the model 0.0 % 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. 6312 reflections ( 97.92 % complete ) and 8780 restraints for refining 3677 atoms. 8031 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1835 (Rfree = 0.000) for 3677 atoms. Found 0 (21 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1730 (Rfree = 0.000) for 3660 atoms. Found 0 (21 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1728 (Rfree = 0.000) for 3648 atoms. Found 0 (21 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1685 (Rfree = 0.000) for 3634 atoms. TimeTaking 43.55