null Sun 23 Dec 22:22:49 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 2gpj-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gpj-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gpj-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-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/2gpj-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-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 22:22:59 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/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-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 224 and 0 Target number of residues in the AU: 224 Target solvent content: 0.6447 Checking the provided sequence file Detected sequence length: 252 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 252 Adjusted target solvent content: 0.60 Input MTZ file: 2gpj-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: 92 Cell parameters: 100.540 100.540 67.510 90.000 90.000 90.000 Input sequence file: 2gpj-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2016 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: 71.093 3.400 Wilson plot Bfac: 74.29 5077 reflections ( 99.53 % complete ) and 0 restraints for refining 2222 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3800 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3872 (Rfree = 0.000) for 2222 atoms. Found 16 (16 requested) and removed 50 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 2.96 Search for helices and strands: 0 residues in 0 chains, 2202 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 7 peptides. Score 0.265 Round 2: 98 peptides, 16 chains. Longest chain 10 peptides. Score 0.365 Round 3: 121 peptides, 21 chains. Longest chain 12 peptides. Score 0.370 Round 4: 127 peptides, 22 chains. Longest chain 10 peptides. Score 0.379 Round 5: 122 peptides, 19 chains. Longest chain 12 peptides. Score 0.418 Taking the results from Round 5 Chains 19, Residues 103, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5077 reflections ( 99.53 % complete ) and 4062 restraints for refining 1833 atoms. 3639 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3556 (Rfree = 0.000) for 1833 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.3599 (Rfree = 0.000) for 1799 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.3532 (Rfree = 0.000) for 1781 atoms. Found 10 (13 requested) and removed 13 (6 requested) atoms. Cycle 4: After refmac, R = 0.3424 (Rfree = 0.000) for 1761 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 5: After refmac, R = 0.3485 (Rfree = 0.000) for 1748 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 2.95 Search for helices and strands: 0 residues in 0 chains, 1773 seeds are put forward Round 1: 93 peptides, 18 chains. Longest chain 11 peptides. Score 0.292 Round 2: 119 peptides, 20 chains. Longest chain 11 peptides. Score 0.382 Round 3: 131 peptides, 21 chains. Longest chain 22 peptides. Score 0.419 Round 4: 136 peptides, 20 chains. Longest chain 19 peptides. Score 0.462 Round 5: 135 peptides, 19 chains. Longest chain 19 peptides. Score 0.477 Taking the results from Round 5 Chains 19, Residues 116, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5077 reflections ( 99.53 % complete ) and 3903 restraints for refining 1809 atoms. 3444 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3400 (Rfree = 0.000) for 1809 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 7: After refmac, R = 0.3179 (Rfree = 0.000) for 1791 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 8: After refmac, R = 0.3088 (Rfree = 0.000) for 1783 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 9: After refmac, R = 0.3105 (Rfree = 0.000) for 1779 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.2955 (Rfree = 0.000) for 1773 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.00 Search for helices and strands: 0 residues in 0 chains, 1837 seeds are put forward Round 1: 131 peptides, 27 chains. Longest chain 10 peptides. Score 0.292 Round 2: 143 peptides, 24 chains. Longest chain 13 peptides. Score 0.413 Round 3: 142 peptides, 27 chains. Longest chain 8 peptides. Score 0.347 Round 4: 137 peptides, 22 chains. Longest chain 11 peptides. Score 0.426 Round 5: 134 peptides, 23 chains. Longest chain 8 peptides. Score 0.392 Taking the results from Round 4 Chains 22, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5077 reflections ( 99.53 % complete ) and 4084 restraints for refining 1833 atoms. 3646 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3238 (Rfree = 0.000) for 1833 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 12: After refmac, R = 0.3139 (Rfree = 0.000) for 1821 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 13: After refmac, R = 0.3090 (Rfree = 0.000) for 1814 atoms. Found 10 (13 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.2964 (Rfree = 0.000) for 1803 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.2898 (Rfree = 0.000) for 1797 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 2.94 Search for helices and strands: 0 residues in 0 chains, 1852 seeds are put forward Round 1: 114 peptides, 22 chains. Longest chain 9 peptides. Score 0.313 Round 2: 127 peptides, 21 chains. Longest chain 12 peptides. Score 0.400 Round 3: 130 peptides, 22 chains. Longest chain 12 peptides. Score 0.393 Round 4: 133 peptides, 20 chains. Longest chain 11 peptides. Score 0.448 Round 5: 140 peptides, 21 chains. Longest chain 16 peptides. Score 0.460 Taking the results from Round 5 Chains 21, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5077 reflections ( 99.53 % complete ) and 4026 restraints for refining 1833 atoms. 3571 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3108 (Rfree = 0.000) for 1833 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 17: After refmac, R = 0.2927 (Rfree = 0.000) for 1821 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.2823 (Rfree = 0.000) for 1821 atoms. Found 10 (13 requested) and removed 9 (6 requested) atoms. Cycle 19: After refmac, R = 0.2836 (Rfree = 0.000) for 1814 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2530 (Rfree = 0.000) for 1821 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 2.99 Search for helices and strands: 0 residues in 0 chains, 1866 seeds are put forward Round 1: 109 peptides, 23 chains. Longest chain 9 peptides. Score 0.264 Round 2: 124 peptides, 22 chains. Longest chain 10 peptides. Score 0.364 Round 3: 124 peptides, 22 chains. Longest chain 10 peptides. Score 0.364 Round 4: 118 peptides, 19 chains. Longest chain 12 peptides. Score 0.399 Round 5: 126 peptides, 21 chains. Longest chain 10 peptides. Score 0.395 Taking the results from Round 4 Chains 19, Residues 99, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5077 reflections ( 99.53 % complete ) and 4113 restraints for refining 1833 atoms. 3722 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3091 (Rfree = 0.000) for 1833 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 22: After refmac, R = 0.3014 (Rfree = 0.000) for 1830 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.3085 (Rfree = 0.000) for 1822 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 24: After refmac, R = 0.2965 (Rfree = 0.000) for 1820 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.2884 (Rfree = 0.000) for 1823 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 2.94 Search for helices and strands: 0 residues in 0 chains, 1881 seeds are put forward Round 1: 98 peptides, 20 chains. Longest chain 7 peptides. Score 0.273 Round 2: 128 peptides, 23 chains. Longest chain 10 peptides. Score 0.362 Round 3: 122 peptides, 21 chains. Longest chain 10 peptides. Score 0.375 Round 4: 128 peptides, 20 chains. Longest chain 10 peptides. Score 0.425 Round 5: 130 peptides, 21 chains. Longest chain 10 peptides. Score 0.414 Taking the results from Round 4 Chains 20, Residues 108, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5077 reflections ( 99.53 % complete ) and 3939 restraints for refining 1833 atoms. 3490 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3091 (Rfree = 0.000) for 1833 atoms. Found 11 (13 requested) and removed 15 (6 requested) atoms. Cycle 27: After refmac, R = 0.2897 (Rfree = 0.000) for 1818 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. Cycle 28: After refmac, R = 0.2805 (Rfree = 0.000) for 1814 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2653 (Rfree = 0.000) for 1811 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.2549 (Rfree = 0.000) for 1805 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 2.98 Search for helices and strands: 0 residues in 0 chains, 1840 seeds are put forward Round 1: 103 peptides, 20 chains. Longest chain 8 peptides. Score 0.300 Round 2: 119 peptides, 20 chains. Longest chain 9 peptides. Score 0.382 Round 3: 127 peptides, 22 chains. Longest chain 10 peptides. Score 0.379 Round 4: 121 peptides, 19 chains. Longest chain 12 peptides. Score 0.413 Round 5: 116 peptides, 18 chains. Longest chain 10 peptides. Score 0.410 Taking the results from Round 4 Chains 19, Residues 102, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5077 reflections ( 99.53 % complete ) and 3878 restraints for refining 1833 atoms. 3445 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2945 (Rfree = 0.000) for 1833 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 32: After refmac, R = 0.2803 (Rfree = 0.000) for 1830 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2828 (Rfree = 0.000) for 1830 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.2702 (Rfree = 0.000) for 1835 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.2587 (Rfree = 0.000) for 1836 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 2.97 Search for helices and strands: 0 residues in 0 chains, 1858 seeds are put forward Round 1: 113 peptides, 24 chains. Longest chain 7 peptides. Score 0.263 Round 2: 114 peptides, 22 chains. Longest chain 10 peptides. Score 0.313 Round 3: 112 peptides, 19 chains. Longest chain 10 peptides. Score 0.369 Round 4: 124 peptides, 23 chains. Longest chain 11 peptides. Score 0.342 Round 5: 126 peptides, 21 chains. Longest chain 13 peptides. Score 0.395 Taking the results from Round 5 Chains 21, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5077 reflections ( 99.53 % complete ) and 4010 restraints for refining 1833 atoms. 3611 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2724 (Rfree = 0.000) for 1833 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. Cycle 37: After refmac, R = 0.2798 (Rfree = 0.000) for 1826 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.2718 (Rfree = 0.000) for 1824 atoms. Found 10 (13 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.2734 (Rfree = 0.000) for 1823 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.2541 (Rfree = 0.000) for 1823 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 2.97 Search for helices and strands: 0 residues in 0 chains, 1841 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.247 Round 2: 93 peptides, 18 chains. Longest chain 8 peptides. Score 0.292 Round 3: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.349 Round 4: 106 peptides, 19 chains. Longest chain 10 peptides. Score 0.338 Round 5: 117 peptides, 20 chains. Longest chain 10 peptides. Score 0.372 Taking the results from Round 5 Chains 20, Residues 97, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5077 reflections ( 99.53 % complete ) and 3913 restraints for refining 1833 atoms. 3492 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2859 (Rfree = 0.000) for 1833 atoms. Found 11 (13 requested) and removed 10 (6 requested) atoms. Cycle 42: After refmac, R = 0.2750 (Rfree = 0.000) for 1830 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.2709 (Rfree = 0.000) for 1834 atoms. Found 9 (13 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2643 (Rfree = 0.000) for 1832 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.2628 (Rfree = 0.000) for 1828 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.00 Search for helices and strands: 0 residues in 0 chains, 1843 seeds are put forward Round 1: 107 peptides, 23 chains. Longest chain 7 peptides. Score 0.253 Round 2: 117 peptides, 23 chains. Longest chain 9 peptides. Score 0.307 Round 3: 112 peptides, 21 chains. Longest chain 9 peptides. Score 0.325 Round 4: 115 peptides, 23 chains. Longest chain 9 peptides. Score 0.296 Round 5: 116 peptides, 21 chains. Longest chain 10 peptides. Score 0.345 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 95, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2gpj-3_warpNtrace.pdb as input Building loops using Loopy2018 21 chains (95 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5077 reflections ( 99.53 % complete ) and 3954 restraints for refining 1833 atoms. 3573 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2943 (Rfree = 0.000) for 1833 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.3060 (Rfree = 0.000) for 1820 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2907 (Rfree = 0.000) for 1806 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2783 (Rfree = 0.000) for 1794 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:55:59 GMT 2018 Job finished. TimeTaking 33.15 Used memory is bytes: 11175648