Tue 25 Dec 19:27:57 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 1vpy-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpy-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpy-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-3.2-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/1vpy-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-3.2-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 ============================================================ Tue 25 Dec 19:28:06 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/1vpy-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-3.2-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 276 and 0 Target number of residues in the AU: 276 Target solvent content: 0.6205 Checking the provided sequence file Detected sequence length: 289 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 289 Adjusted target solvent content: 0.60 Input MTZ file: 1vpy-3.2-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: 170 Cell parameters: 114.136 114.136 52.333 90.000 90.000 120.000 Input sequence file: 1vpy-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2312 target number of atoms Had to go as low as 0.80 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: 98.845 3.200 Wilson plot Bfac: 61.50 6573 reflections ( 99.82 % complete ) and 0 restraints for refining 2588 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3058 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2741 (Rfree = 0.000) for 2588 atoms. Found 23 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 2.78 Search for helices and strands: 0 residues in 0 chains, 2657 seeds are put forward Round 1: 171 peptides, 26 chains. Longest chain 16 peptides. Score 0.466 Round 2: 184 peptides, 21 chains. Longest chain 23 peptides. Score 0.589 Round 3: 194 peptides, 21 chains. Longest chain 21 peptides. Score 0.620 Round 4: 195 peptides, 19 chains. Longest chain 41 peptides. Score 0.650 Round 5: 199 peptides, 22 chains. Longest chain 23 peptides. Score 0.621 Taking the results from Round 4 Chains 22, Residues 176, Estimated correctness of the model 53.8 % 3 chains (67 residues) have been docked in sequence ------------------------------------------------------ 6573 reflections ( 99.82 % complete ) and 3933 restraints for refining 2111 atoms. 2966 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2594 (Rfree = 0.000) for 2111 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 2: After refmac, R = 0.2401 (Rfree = 0.000) for 2085 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 3: After refmac, R = 0.2278 (Rfree = 0.000) for 2077 atoms. Found 12 (18 requested) and removed 10 (9 requested) atoms. Cycle 4: After refmac, R = 0.2195 (Rfree = 0.000) for 2067 atoms. Found 10 (18 requested) and removed 10 (9 requested) atoms. Cycle 5: After refmac, R = 0.2160 (Rfree = 0.000) for 2059 atoms. Found 9 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 2.77 Search for helices and strands: 0 residues in 0 chains, 2130 seeds are put forward Round 1: 193 peptides, 22 chains. Longest chain 21 peptides. Score 0.603 Round 2: 192 peptides, 18 chains. Longest chain 29 peptides. Score 0.654 Round 3: 194 peptides, 18 chains. Longest chain 31 peptides. Score 0.660 Round 4: 196 peptides, 17 chains. Longest chain 27 peptides. Score 0.678 Round 5: 188 peptides, 17 chains. Longest chain 24 peptides. Score 0.657 Taking the results from Round 4 Chains 20, Residues 179, Estimated correctness of the model 60.4 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6573 reflections ( 99.82 % complete ) and 4200 restraints for refining 2110 atoms. 3302 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2557 (Rfree = 0.000) for 2110 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2285 (Rfree = 0.000) for 2094 atoms. Found 16 (18 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2161 (Rfree = 0.000) for 2090 atoms. Found 12 (18 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2036 (Rfree = 0.000) for 2088 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.1999 (Rfree = 0.000) for 2077 atoms. Found 9 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 2.73 Search for helices and strands: 0 residues in 0 chains, 2156 seeds are put forward Round 1: 180 peptides, 19 chains. Longest chain 26 peptides. Score 0.606 Round 2: 187 peptides, 18 chains. Longest chain 25 peptides. Score 0.640 Round 3: 195 peptides, 19 chains. Longest chain 26 peptides. Score 0.650 Round 4: 204 peptides, 18 chains. Longest chain 27 peptides. Score 0.686 Round 5: 207 peptides, 20 chains. Longest chain 26 peptides. Score 0.669 Taking the results from Round 4 Chains 21, Residues 186, Estimated correctness of the model 62.2 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6573 reflections ( 99.82 % complete ) and 4399 restraints for refining 2099 atoms. 3587 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2445 (Rfree = 0.000) for 2099 atoms. Found 15 (18 requested) and removed 26 (9 requested) atoms. Cycle 12: After refmac, R = 0.2296 (Rfree = 0.000) for 2083 atoms. Found 12 (18 requested) and removed 9 (9 requested) atoms. Cycle 13: After refmac, R = 0.2257 (Rfree = 0.000) for 2083 atoms. Found 13 (18 requested) and removed 13 (9 requested) atoms. Cycle 14: After refmac, R = 0.2367 (Rfree = 0.000) for 2081 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2077 (Rfree = 0.000) for 2087 atoms. Found 10 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 2.74 Search for helices and strands: 0 residues in 0 chains, 2144 seeds are put forward Round 1: 177 peptides, 19 chains. Longest chain 25 peptides. Score 0.596 Round 2: 191 peptides, 14 chains. Longest chain 34 peptides. Score 0.703 Round 3: 194 peptides, 14 chains. Longest chain 41 peptides. Score 0.710 Round 4: 195 peptides, 16 chains. Longest chain 29 peptides. Score 0.688 Round 5: 184 peptides, 16 chains. Longest chain 25 peptides. Score 0.659 Taking the results from Round 3 Chains 14, Residues 180, Estimated correctness of the model 67.3 % 4 chains (89 residues) have been docked in sequence Building loops using Loopy2018 14 chains (180 residues) following loop building 4 chains (89 residues) in sequence following loop building ------------------------------------------------------ 6573 reflections ( 99.82 % complete ) and 3650 restraints for refining 2111 atoms. 2528 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2500 (Rfree = 0.000) for 2111 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2335 (Rfree = 0.000) for 2106 atoms. Found 9 (18 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2170 (Rfree = 0.000) for 2094 atoms. Found 7 (17 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2219 (Rfree = 0.000) for 2083 atoms. Found 17 (17 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.2036 (Rfree = 0.000) for 2087 atoms. Found 9 (17 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 2.74 Search for helices and strands: 0 residues in 0 chains, 2146 seeds are put forward Round 1: 194 peptides, 20 chains. Longest chain 22 peptides. Score 0.633 Round 2: 212 peptides, 15 chains. Longest chain 27 peptides. Score 0.740 Round 3: 201 peptides, 14 chains. Longest chain 36 peptides. Score 0.727 Round 4: 206 peptides, 18 chains. Longest chain 33 peptides. Score 0.691 Round 5: 202 peptides, 20 chains. Longest chain 21 peptides. Score 0.656 Taking the results from Round 2 Chains 17, Residues 197, Estimated correctness of the model 73.2 % 4 chains (82 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 197 A and 200 A 16 chains (199 residues) following loop building 3 chains (84 residues) in sequence following loop building ------------------------------------------------------ 6573 reflections ( 99.82 % complete ) and 3589 restraints for refining 2111 atoms. 2441 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2208 (Rfree = 0.000) for 2111 atoms. Found 16 (16 requested) and removed 19 (9 requested) atoms. Cycle 22: After refmac, R = 0.2171 (Rfree = 0.000) for 2105 atoms. Found 16 (16 requested) and removed 16 (9 requested) atoms. Cycle 23: After refmac, R = 0.2235 (Rfree = 0.000) for 2097 atoms. Found 15 (15 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2135 (Rfree = 0.000) for 2094 atoms. Found 15 (15 requested) and removed 14 (9 requested) atoms. Cycle 25: After refmac, R = 0.2131 (Rfree = 0.000) for 2089 atoms. Found 15 (15 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.73 Search for helices and strands: 0 residues in 0 chains, 2161 seeds are put forward Round 1: 191 peptides, 23 chains. Longest chain 22 peptides. Score 0.582 Round 2: 202 peptides, 20 chains. Longest chain 26 peptides. Score 0.656 Round 3: 205 peptides, 22 chains. Longest chain 32 peptides. Score 0.638 Round 4: 204 peptides, 18 chains. Longest chain 25 peptides. Score 0.686 Round 5: 201 peptides, 20 chains. Longest chain 22 peptides. Score 0.653 Taking the results from Round 4 Chains 22, Residues 186, Estimated correctness of the model 62.2 % 5 chains (83 residues) have been docked in sequence ------------------------------------------------------ 6573 reflections ( 99.82 % complete ) and 3706 restraints for refining 2111 atoms. 2624 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2363 (Rfree = 0.000) for 2111 atoms. Found 14 (14 requested) and removed 15 (9 requested) atoms. Cycle 27: After refmac, R = 0.2187 (Rfree = 0.000) for 2099 atoms. Found 14 (14 requested) and removed 10 (9 requested) atoms. Cycle 28: After refmac, R = 0.1995 (Rfree = 0.000) for 2094 atoms. Found 11 (14 requested) and removed 11 (9 requested) atoms. Cycle 29: After refmac, R = 0.1918 (Rfree = 0.000) for 2092 atoms. Found 3 (14 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.1945 (Rfree = 0.000) for 2079 atoms. Found 5 (14 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.12 2.73 Search for helices and strands: 0 residues in 0 chains, 2154 seeds are put forward Round 1: 178 peptides, 19 chains. Longest chain 19 peptides. Score 0.600 Round 2: 199 peptides, 18 chains. Longest chain 20 peptides. Score 0.673 Round 3: 186 peptides, 19 chains. Longest chain 19 peptides. Score 0.624 Round 4: 198 peptides, 18 chains. Longest chain 21 peptides. Score 0.671 Round 5: 184 peptides, 19 chains. Longest chain 23 peptides. Score 0.618 Taking the results from Round 2 Chains 18, Residues 181, Estimated correctness of the model 59.2 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6573 reflections ( 99.82 % complete ) and 4360 restraints for refining 2111 atoms. 3563 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2642 (Rfree = 0.000) for 2111 atoms. Found 14 (14 requested) and removed 19 (9 requested) atoms. Cycle 32: After refmac, R = 0.2505 (Rfree = 0.000) for 2099 atoms. Found 14 (14 requested) and removed 15 (9 requested) atoms. Cycle 33: After refmac, R = 0.2579 (Rfree = 0.000) for 2093 atoms. Found 14 (14 requested) and removed 20 (9 requested) atoms. Cycle 34: After refmac, R = 0.2127 (Rfree = 0.000) for 2079 atoms. Found 14 (14 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.2009 (Rfree = 0.000) for 2078 atoms. Found 12 (14 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.10 2.71 Search for helices and strands: 0 residues in 0 chains, 2156 seeds are put forward Round 1: 185 peptides, 21 chains. Longest chain 36 peptides. Score 0.592 Round 2: 201 peptides, 20 chains. Longest chain 23 peptides. Score 0.653 Round 3: 207 peptides, 18 chains. Longest chain 38 peptides. Score 0.694 Round 4: 191 peptides, 17 chains. Longest chain 38 peptides. Score 0.665 Round 5: 188 peptides, 19 chains. Longest chain 22 peptides. Score 0.630 Taking the results from Round 3 Chains 19, Residues 189, Estimated correctness of the model 63.9 % 3 chains (64 residues) have been docked in sequence ------------------------------------------------------ 6573 reflections ( 99.82 % complete ) and 3754 restraints for refining 2109 atoms. 2745 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2606 (Rfree = 0.000) for 2109 atoms. Found 14 (14 requested) and removed 17 (9 requested) atoms. Cycle 37: After refmac, R = 0.2405 (Rfree = 0.000) for 2099 atoms. Found 14 (14 requested) and removed 14 (9 requested) atoms. Cycle 38: After refmac, R = 0.2402 (Rfree = 0.000) for 2081 atoms. Found 14 (14 requested) and removed 10 (9 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2332 (Rfree = 0.000) for 2074 atoms. Found 14 (14 requested) and removed 18 (9 requested) atoms. Cycle 40: After refmac, R = 0.2236 (Rfree = 0.000) for 2061 atoms. Found 14 (14 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.74 Search for helices and strands: 0 residues in 0 chains, 2128 seeds are put forward Round 1: 177 peptides, 20 chains. Longest chain 25 peptides. Score 0.582 Round 2: 188 peptides, 18 chains. Longest chain 26 peptides. Score 0.643 Round 3: 185 peptides, 18 chains. Longest chain 31 peptides. Score 0.635 Round 4: 191 peptides, 15 chains. Longest chain 45 peptides. Score 0.691 Round 5: 181 peptides, 18 chains. Longest chain 24 peptides. Score 0.623 Taking the results from Round 4 Chains 17, Residues 176, Estimated correctness of the model 63.2 % 3 chains (65 residues) have been docked in sequence ------------------------------------------------------ 6573 reflections ( 99.82 % complete ) and 3891 restraints for refining 2111 atoms. 2923 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2554 (Rfree = 0.000) for 2111 atoms. Found 14 (14 requested) and removed 15 (9 requested) atoms. Cycle 42: After refmac, R = 0.2442 (Rfree = 0.000) for 2101 atoms. Found 14 (14 requested) and removed 12 (9 requested) atoms. Cycle 43: After refmac, R = 0.2074 (Rfree = 0.000) for 2095 atoms. Found 10 (14 requested) and removed 10 (9 requested) atoms. Cycle 44: After refmac, R = 0.2016 (Rfree = 0.000) for 2088 atoms. Found 10 (14 requested) and removed 11 (9 requested) atoms. Cycle 45: After refmac, R = 0.1899 (Rfree = 0.000) for 2087 atoms. Found 4 (14 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 2.73 Search for helices and strands: 0 residues in 0 chains, 2153 seeds are put forward Round 1: 160 peptides, 16 chains. Longest chain 29 peptides. Score 0.587 Round 2: 189 peptides, 18 chains. Longest chain 27 peptides. Score 0.646 Round 3: 181 peptides, 16 chains. Longest chain 30 peptides. Score 0.651 Round 4: 184 peptides, 15 chains. Longest chain 43 peptides. Score 0.672 Round 5: 186 peptides, 16 chains. Longest chain 29 peptides. Score 0.665 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 169, Estimated correctness of the model 59.0 % 2 chains (60 residues) have been docked in sequence Sequence coverage is 35 % Consider running further cycles of model building using 1vpy-3_warpNtrace.pdb as input Building loops using Loopy2018 18 chains (169 residues) following loop building 2 chains (60 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6573 reflections ( 99.82 % complete ) and 4016 restraints for refining 2110 atoms. 3101 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3106 (Rfree = 0.000) for 2110 atoms. Found 0 (14 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2346 (Rfree = 0.000) for 2094 atoms. Found 0 (14 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2156 (Rfree = 0.000) for 2083 atoms. Found 0 (14 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2064 (Rfree = 0.000) for 2072 atoms. Found 0 (14 requested) and removed 9 (9 requested) atoms. Writing output files ... TimeTaking 50.45