Sun 23 Dec 22:22:46 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 2hoe-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hoe-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hoe-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-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/2hoe-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-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 22:22:56 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/2hoe-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-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 248 and 0 Target number of residues in the AU: 248 Target solvent content: 0.6590 Checking the provided sequence file Detected sequence length: 380 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 380 Adjusted target solvent content: 0.48 Input MTZ file: 2hoe-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: 151 Cell parameters: 62.599 62.599 173.950 90.000 90.000 120.000 Input sequence file: 2hoe-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3040 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 57.983 3.400 Wilson plot Bfac: 84.04 5328 reflections ( 95.02 % complete ) and 0 restraints for refining 3376 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3293 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3020 (Rfree = 0.000) for 3376 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 3445 seeds are put forward Round 1: 148 peptides, 27 chains. Longest chain 14 peptides. Score 0.355 Round 2: 185 peptides, 26 chains. Longest chain 28 peptides. Score 0.517 Round 3: 218 peptides, 27 chains. Longest chain 34 peptides. Score 0.609 Round 4: 220 peptides, 28 chains. Longest chain 35 peptides. Score 0.602 Round 5: 229 peptides, 27 chains. Longest chain 38 peptides. Score 0.641 Taking the results from Round 5 Chains 27, Residues 202, Estimated correctness of the model 41.5 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 5328 reflections ( 95.02 % complete ) and 6043 restraints for refining 2763 atoms. 5120 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2498 (Rfree = 0.000) for 2763 atoms. Found 10 (20 requested) and removed 32 (10 requested) atoms. Cycle 2: After refmac, R = 0.2321 (Rfree = 0.000) for 2707 atoms. Found 8 (20 requested) and removed 17 (10 requested) atoms. Cycle 3: After refmac, R = 0.2446 (Rfree = 0.000) for 2671 atoms. Found 6 (20 requested) and removed 19 (10 requested) atoms. Cycle 4: After refmac, R = 0.2166 (Rfree = 0.000) for 2640 atoms. Found 7 (20 requested) and removed 13 (10 requested) atoms. Cycle 5: After refmac, R = 0.2283 (Rfree = 0.000) for 2624 atoms. Found 6 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 2690 seeds are put forward Round 1: 177 peptides, 26 chains. Longest chain 21 peptides. Score 0.488 Round 2: 207 peptides, 24 chains. Longest chain 41 peptides. Score 0.617 Round 3: 208 peptides, 25 chains. Longest chain 21 peptides. Score 0.607 Round 4: 196 peptides, 25 chains. Longest chain 23 peptides. Score 0.569 Round 5: 213 peptides, 25 chains. Longest chain 29 peptides. Score 0.621 Taking the results from Round 5 Chains 28, Residues 188, Estimated correctness of the model 35.4 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5328 reflections ( 95.02 % complete ) and 6133 restraints for refining 2738 atoms. 5318 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2284 (Rfree = 0.000) for 2738 atoms. Found 16 (20 requested) and removed 35 (10 requested) atoms. Cycle 7: After refmac, R = 0.2232 (Rfree = 0.000) for 2704 atoms. Found 8 (20 requested) and removed 21 (10 requested) atoms. Cycle 8: After refmac, R = 0.2060 (Rfree = 0.000) for 2671 atoms. Found 4 (20 requested) and removed 15 (10 requested) atoms. Cycle 9: After refmac, R = 0.2180 (Rfree = 0.000) for 2644 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. Cycle 10: After refmac, R = 0.1850 (Rfree = 0.000) for 2627 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 2720 seeds are put forward Round 1: 167 peptides, 27 chains. Longest chain 17 peptides. Score 0.433 Round 2: 215 peptides, 25 chains. Longest chain 31 peptides. Score 0.627 Round 3: 210 peptides, 25 chains. Longest chain 31 peptides. Score 0.612 Round 4: 212 peptides, 27 chains. Longest chain 19 peptides. Score 0.591 Round 5: 199 peptides, 23 chains. Longest chain 31 peptides. Score 0.607 Taking the results from Round 2 Chains 27, Residues 190, Estimated correctness of the model 37.2 % 4 chains (54 residues) have been docked in sequence ------------------------------------------------------ 5328 reflections ( 95.02 % complete ) and 5701 restraints for refining 2716 atoms. 4790 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2175 (Rfree = 0.000) for 2716 atoms. Found 16 (20 requested) and removed 46 (10 requested) atoms. Cycle 12: After refmac, R = 0.2080 (Rfree = 0.000) for 2678 atoms. Found 8 (20 requested) and removed 18 (10 requested) atoms. Cycle 13: After refmac, R = 0.2052 (Rfree = 0.000) for 2662 atoms. Found 1 (20 requested) and removed 20 (10 requested) atoms. Cycle 14: After refmac, R = 0.1979 (Rfree = 0.000) for 2638 atoms. Found 6 (19 requested) and removed 14 (9 requested) atoms. Cycle 15: After refmac, R = 0.1947 (Rfree = 0.000) for 2624 atoms. Found 5 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.58 Search for helices and strands: 0 residues in 0 chains, 2702 seeds are put forward Round 1: 178 peptides, 27 chains. Longest chain 23 peptides. Score 0.475 Round 2: 203 peptides, 22 chains. Longest chain 45 peptides. Score 0.632 Round 3: 199 peptides, 28 chains. Longest chain 24 peptides. Score 0.535 Round 4: 203 peptides, 22 chains. Longest chain 27 peptides. Score 0.632 Round 5: 201 peptides, 24 chains. Longest chain 32 peptides. Score 0.599 Taking the results from Round 4 Chains 23, Residues 181, Estimated correctness of the model 38.8 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5328 reflections ( 95.02 % complete ) and 6046 restraints for refining 2764 atoms. 5306 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2084 (Rfree = 0.000) for 2764 atoms. Found 10 (20 requested) and removed 24 (10 requested) atoms. Cycle 17: After refmac, R = 0.1974 (Rfree = 0.000) for 2740 atoms. Found 1 (20 requested) and removed 15 (10 requested) atoms. Cycle 18: After refmac, R = 0.1893 (Rfree = 0.000) for 2723 atoms. Found 6 (20 requested) and removed 22 (10 requested) atoms. Cycle 19: After refmac, R = 0.1713 (Rfree = 0.000) for 2702 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.1658 (Rfree = 0.000) for 2693 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 2781 seeds are put forward Round 1: 172 peptides, 25 chains. Longest chain 23 peptides. Score 0.486 Round 2: 200 peptides, 28 chains. Longest chain 27 peptides. Score 0.538 Round 3: 203 peptides, 30 chains. Longest chain 22 peptides. Score 0.518 Round 4: 206 peptides, 29 chains. Longest chain 18 peptides. Score 0.543 Round 5: 215 peptides, 27 chains. Longest chain 46 peptides. Score 0.600 Taking the results from Round 5 Chains 27, Residues 188, Estimated correctness of the model 28.7 % 2 chains (48 residues) have been docked in sequence ------------------------------------------------------ 5328 reflections ( 95.02 % complete ) and 5650 restraints for refining 2764 atoms. 4754 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2264 (Rfree = 0.000) for 2764 atoms. Found 10 (20 requested) and removed 59 (10 requested) atoms. Cycle 22: After refmac, R = 0.2032 (Rfree = 0.000) for 2705 atoms. Found 9 (20 requested) and removed 23 (10 requested) atoms. Cycle 23: After refmac, R = 0.1901 (Rfree = 0.000) for 2690 atoms. Found 3 (20 requested) and removed 17 (10 requested) atoms. Cycle 24: After refmac, R = 0.1835 (Rfree = 0.000) for 2674 atoms. Found 3 (20 requested) and removed 13 (10 requested) atoms. Cycle 25: After refmac, R = 0.1794 (Rfree = 0.000) for 2662 atoms. Found 1 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 2752 seeds are put forward Round 1: 157 peptides, 25 chains. Longest chain 22 peptides. Score 0.428 Round 2: 174 peptides, 25 chains. Longest chain 23 peptides. Score 0.493 Round 3: 190 peptides, 27 chains. Longest chain 20 peptides. Score 0.519 Round 4: 192 peptides, 23 chains. Longest chain 30 peptides. Score 0.585 Round 5: 184 peptides, 27 chains. Longest chain 20 peptides. Score 0.498 Taking the results from Round 4 Chains 23, Residues 169, Estimated correctness of the model 23.7 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5328 reflections ( 95.02 % complete ) and 6136 restraints for refining 2763 atoms. 5459 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2009 (Rfree = 0.000) for 2763 atoms. Found 6 (20 requested) and removed 18 (10 requested) atoms. Cycle 27: After refmac, R = 0.2305 (Rfree = 0.000) for 2743 atoms. Found 8 (20 requested) and removed 14 (10 requested) atoms. Cycle 28: After refmac, R = 0.1816 (Rfree = 0.000) for 2728 atoms. Found 7 (20 requested) and removed 15 (10 requested) atoms. Cycle 29: After refmac, R = 0.1838 (Rfree = 0.000) for 2714 atoms. Found 4 (20 requested) and removed 12 (10 requested) atoms. Cycle 30: After refmac, R = 0.1884 (Rfree = 0.000) for 2701 atoms. Found 5 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 2781 seeds are put forward Round 1: 165 peptides, 30 chains. Longest chain 15 peptides. Score 0.373 Round 2: 193 peptides, 32 chains. Longest chain 20 peptides. Score 0.450 Round 3: 199 peptides, 31 chains. Longest chain 12 peptides. Score 0.488 Round 4: 202 peptides, 29 chains. Longest chain 20 peptides. Score 0.530 Round 5: 206 peptides, 29 chains. Longest chain 20 peptides. Score 0.543 Taking the results from Round 5 Chains 30, Residues 177, Estimated correctness of the model 9.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5328 reflections ( 95.02 % complete ) and 5940 restraints for refining 2764 atoms. 5200 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2212 (Rfree = 0.000) for 2764 atoms. Found 13 (20 requested) and removed 23 (10 requested) atoms. Cycle 32: After refmac, R = 0.1957 (Rfree = 0.000) for 2749 atoms. Found 10 (20 requested) and removed 22 (10 requested) atoms. Cycle 33: After refmac, R = 0.1814 (Rfree = 0.000) for 2731 atoms. Found 4 (20 requested) and removed 12 (10 requested) atoms. Cycle 34: After refmac, R = 0.1995 (Rfree = 0.000) for 2715 atoms. Found 11 (20 requested) and removed 15 (10 requested) atoms. Cycle 35: After refmac, R = 0.1922 (Rfree = 0.000) for 2704 atoms. Found 5 (20 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 2756 seeds are put forward Round 1: 142 peptides, 27 chains. Longest chain 11 peptides. Score 0.329 Round 2: 175 peptides, 27 chains. Longest chain 18 peptides. Score 0.464 Round 3: 160 peptides, 22 chains. Longest chain 15 peptides. Score 0.491 Round 4: 181 peptides, 24 chains. Longest chain 18 peptides. Score 0.534 Round 5: 175 peptides, 27 chains. Longest chain 19 peptides. Score 0.464 Taking the results from Round 4 Chains 26, Residues 157, Estimated correctness of the model 5.7 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 5328 reflections ( 95.02 % complete ) and 5856 restraints for refining 2764 atoms. 5156 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2137 (Rfree = 0.000) for 2764 atoms. Found 10 (20 requested) and removed 30 (10 requested) atoms. Cycle 37: After refmac, R = 0.1992 (Rfree = 0.000) for 2739 atoms. Found 17 (20 requested) and removed 15 (10 requested) atoms. Cycle 38: After refmac, R = 0.2461 (Rfree = 0.000) for 2732 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 39: After refmac, R = 0.1718 (Rfree = 0.000) for 2723 atoms. Found 12 (20 requested) and removed 12 (10 requested) atoms. Cycle 40: After refmac, R = 0.1437 (Rfree = 0.000) for 2720 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.53 Search for helices and strands: 0 residues in 0 chains, 2808 seeds are put forward Round 1: 151 peptides, 29 chains. Longest chain 11 peptides. Score 0.331 Round 2: 158 peptides, 23 chains. Longest chain 16 peptides. Score 0.467 Round 3: 155 peptides, 25 chains. Longest chain 15 peptides. Score 0.420 Round 4: 152 peptides, 23 chains. Longest chain 9 peptides. Score 0.444 Round 5: 151 peptides, 24 chains. Longest chain 11 peptides. Score 0.422 Taking the results from Round 2 Chains 23, Residues 135, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5328 reflections ( 95.02 % complete ) and 6157 restraints for refining 2764 atoms. 5581 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1971 (Rfree = 0.000) for 2764 atoms. Found 9 (20 requested) and removed 31 (10 requested) atoms. Cycle 42: After refmac, R = 0.1743 (Rfree = 0.000) for 2734 atoms. Found 7 (20 requested) and removed 12 (10 requested) atoms. Cycle 43: After refmac, R = 0.1592 (Rfree = 0.000) for 2723 atoms. Found 3 (20 requested) and removed 13 (10 requested) atoms. Cycle 44: After refmac, R = 0.1569 (Rfree = 0.000) for 2713 atoms. Found 3 (20 requested) and removed 13 (10 requested) atoms. Cycle 45: After refmac, R = 0.1543 (Rfree = 0.000) for 2702 atoms. Found 0 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 2776 seeds are put forward Round 1: 115 peptides, 22 chains. Longest chain 11 peptides. Score 0.303 Round 2: 136 peptides, 23 chains. Longest chain 16 peptides. Score 0.378 Round 3: 141 peptides, 22 chains. Longest chain 13 peptides. Score 0.417 Round 4: 144 peptides, 22 chains. Longest chain 14 peptides. Score 0.429 Round 5: 143 peptides, 23 chains. Longest chain 13 peptides. Score 0.407 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 122, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2hoe-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 5328 reflections ( 95.02 % complete ) and 6293 restraints for refining 2764 atoms. 5784 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2052 (Rfree = 0.000) for 2764 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2222 (Rfree = 0.000) for 2745 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2055 (Rfree = 0.000) for 2725 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1988 (Rfree = 0.000) for 2714 atoms. TimeTaking 51.43